From 6869b193a07bb15c24381b0600fe26810ad68518 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 30 Jun 2023 17:58:25 -0600 Subject: [PATCH 01/80] Update bioblend to 1.2.0 (#41787) * Update bioblend to 1.2.0 * Also test importing `bioblend.galaxy.container_resolution` --------- Co-authored-by: Nicola Soranzo --- recipes/bioblend/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml index 5581c0afb9baa9..884a589adf76a4 100644 --- a/recipes/bioblend/meta.yaml +++ b/recipes/bioblend/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.1" %} +{% set version = "1.2.0" %} package: name: bioblend @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz - sha256: 790fd786451978e380392ea8b33ebb224f0b66158c1d584167cecfaefa6bfb58 + sha256: 90be67c5e0dbdb1235fd9a8cb463b5ded1c6a2d6a8303913649068973d037903 build: noarch: python @@ -30,6 +30,7 @@ test: - bioblend - bioblend.galaxy - bioblend.galaxy.config + - bioblend.galaxy.container_resolution - bioblend.galaxy.dataset_collections - bioblend.galaxy.datasets - bioblend.galaxy.datatypes From fecc759d58c6bd87c4f24bb7ae54ddf31c4e9a8d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 30 Jun 2023 19:10:32 -0600 Subject: [PATCH 02/80] Update bactopia-gather to 1.0.3 (#41788) * Update bactopia-gather to 1.0.3 * loosen python pinning --------- Co-authored-by: Robert A. Petit III --- recipes/bactopia-gather/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/bactopia-gather/meta.yaml b/recipes/bactopia-gather/meta.yaml index cd73acc4948603..8e77f2a38a84d3 100644 --- a/recipes/bactopia-gather/meta.yaml +++ b/recipes/bactopia-gather/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: bactopia-gather @@ -10,7 +10,7 @@ build: source: url: https://github.com/bactopia/bactopia-gather/archive/v{{version}}.tar.gz - sha256: e8973fc58ef004803944bdf31ff47cd0acbf3665656f0f45044c0efd96680408 + sha256: a8fb55e78a723f2ff239a2f6e254cccbd38283321b483220622f77c13c82fe9f requirements: run: @@ -18,14 +18,14 @@ requirements: - bbmap >=39.01 - biopython 1.77 - coreutils - - fastq-dl >=2.0.0 + - fastq-dl >=2.0.2 - fastq-scan >=1.0.1 - gsl 2.6 - mash >=2.3 - ncbi-genome-download >=0.3.1 - rename - pigz - - python >=3.9,<3.11 + - python >=3.8,<3.11 - sed - sra-tools >=3.0.1 From bd2eddaef0831950e047d72cf7fd39a60a857173 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 30 Jun 2023 19:40:03 -0600 Subject: [PATCH 03/80] Update bactopia-py to 1.0.4 (#41789) --- recipes/bactopia-py/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml index 00014793637beb..73bb70ae6b0acc 100644 --- a/recipes/bactopia-py/meta.yaml +++ b/recipes/bactopia-py/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bactopia-py" %} -{% set version = "1.0.3" %} +{% set version = "1.0.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz - sha256: ddbd5a4e776ef4a958ceec5bd0e017323a380417420d27ebf9e1cde708104d15 + sha256: c139be0d812f95cf466347ca03f1b4875e2f64038b5c5aec3f33dc438c4a195f build: noarch: python From a934edae76cf8329b1396cc41b03baf708298b2a Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 00:47:56 -0600 Subject: [PATCH 04/80] Update galaxy-objectstore to 23.0.4 (#41680) * Update galaxy-objectstore to 23.0.3 * Update galaxy-objectstore to 23.0.4 --- recipes/galaxy-objectstore/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml index b1fbd17c70a1d7..1a049920411e69 100644 --- a/recipes/galaxy-objectstore/meta.yaml +++ b/recipes/galaxy-objectstore/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "23.0.2" %} -{% set sha256 = "201e8cb4426b6b0b42f675968a54d717c6159e52c9020192ed58838060f6991d" %} +{% set version = "23.0.4" %} +{% set sha256 = "6f57f8503dce9cbcff4b418a94026cf293f4cdaab654d53e2ec0f306bb931808" %} {% set galaxy_version = version.split(".")[:2]|join(".") %} package: From c952c64367f6043e7468c6d11eb275359acaf90b Mon Sep 17 00:00:00 2001 From: Kristian Ullrich Date: Sat, 1 Jul 2023 09:13:22 +0200 Subject: [PATCH 05/80] Add CRBHits (#41776) * Create r-crbhits * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml --- recipes/r-crbhits/build.sh | 22 ++++++++++ recipes/r-crbhits/meta.yaml | 84 +++++++++++++++++++++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 recipes/r-crbhits/build.sh create mode 100644 recipes/r-crbhits/meta.yaml diff --git a/recipes/r-crbhits/build.sh b/recipes/r-crbhits/build.sh new file mode 100644 index 00000000000000..df943f40e3e3d2 --- /dev/null +++ b/recipes/r-crbhits/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# 'Autobrew' is being used by more and more packages these days +# to grab static libraries from Homebrew bottles. These bottles +# are fetched via Homebrew's --force-bottle option which grabs +# a bottle for the build machine which may not be macOS 10.9. +# Also, we want to use conda packages (and shared libraries) for +# these 'system' dependencies. See: +# https://github.com/jeroen/autobrew/issues/3 +export DISABLE_AUTOBREW=1 + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} + +# Add more build steps here, if they are necessary. + +# See +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-crbhits/meta.yaml b/recipes/r-crbhits/meta.yaml new file mode 100644 index 00000000000000..9d7a47a1b77e8a --- /dev/null +++ b/recipes/r-crbhits/meta.yaml @@ -0,0 +1,84 @@ +{% set name = "r-crbhits" %} +{% set version = "0.0.4" %} + +package: + name: "{{ name }}" + version: "{{ version }}" + +source: + url: https://github.com/kullrich/CRBHits/archive/refs/tags/v{{ version }}.tar.gz + sha256: a44ae1f6f16bf321adf9a0342e3f577ea8322e0f49e507908254f2229c55cc00 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + - last + - kakscalculator2 + - dagchainer + host: + - r-base + - bioconductor-biostrings + - bioconductor-msa2dist + - r-curl + - r-doParallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gridExtra + - r-readr + - r-rlang + - r-seqinr + - r-stringr + - r-tidyr + - r-ape + - r-markdown + - r-knitr + - r-devtools + - r-stringi + - r-testthat + - r-tibble + run: + - r-base + - bioconductor-biostrings + - bioconductor-msa2dist + - r-curl + - r-doParallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gridExtra + - r-readr + - r-rlang + - r-seqinr + - r-stringr + - r-tidyr + - r-ape + - r-markdown + - r-knitr + - r-devtools + - r-stringi + - r-testthat + - r-tibble + +test: + commands: + - $R -e "library('CRBHits')" # [not win] + - "\"%R%\" -e \"library('CRBHits')\"" # [win] + +about: + home: https://github.com/kullrich/CRBHits + license: MIT + summary: "CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R." + description: "CRBHits is a reimplementation of the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast in R. It covers all necessary steps from CRBHit pair calculation to Codon Alignments and Ka/Ks. (see [Ullrich (2020) ])" + license_family: MIT +extra: + identifiers: + - doi:10.21105/joss.02424 From ab7b8a2a0fc06b7a06014e1ecb6c6b27ef098c5d Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:14:45 -0500 Subject: [PATCH 06/80] Update parasail-python to 1.3.4 (#41763) * Update parasail-python to 1.3.4 * add back CXX compiler * add skip: True for python < 3.7 --- .../parasail-python/darwin-libtool-name.patch | 4 +-- recipes/parasail-python/meta.yaml | 31 +++++++++++-------- 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/recipes/parasail-python/darwin-libtool-name.patch b/recipes/parasail-python/darwin-libtool-name.patch index 93ad1287ad0acc..a182af5352e3f9 100644 --- a/recipes/parasail-python/darwin-libtool-name.patch +++ b/recipes/parasail-python/darwin-libtool-name.patch @@ -1,7 +1,7 @@ diff --git setup.py setup.py index d8344f8..961803d 100644 ---- setup.py -+++ setup.py +--- a/setup.py ++++ b/setup.py @@ -158,9 +158,9 @@ def run_autoreconf(root): all_good = True tools = ['perl', 'm4', 'autoconf', 'automake', 'libtoolize', 'autoreconf'] diff --git a/recipes/parasail-python/meta.yaml b/recipes/parasail-python/meta.yaml index 26377337a0e4c2..9806e254863e3d 100644 --- a/recipes/parasail-python/meta.yaml +++ b/recipes/parasail-python/meta.yaml @@ -1,39 +1,39 @@ {% set name = "parasail-python" %} -{% set version = "1.3.3" %} -{% set sha256 = "e11177977961650956c9d94f9d0f46af26fc9b2c91034a438e4104a27316c355" %} +{% set version = "1.3.4" %} +{% set sha256 = "d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f" %} package: - name: "{{ name|lower }}" - version: "{{ version }}" + name: {{ name }} + version: {{ version }} source: - url: https://github.com/jeffdaily/parasail-python/archive/v{{ version }}.tar.gz - sha256: "{{ sha256 }}" + url: https://pypi.io/packages/source/{{ name[0] }}/parasail/parasail-{{ version }}.tar.gz + sha256: {{ sha256 }} patches: - darwin-libtool-name.patch build: - number: 2 - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + number: 0 + skip: True # [py < 37] + script: {{ PYTHON }} -m pip install . --use-pep517 -vv requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - m4 + - make - autoconf - automake - libtool - - make host: - python - pip - - zlib - wheel + - zlib run: - python - numpy - - wheel test: imports: @@ -41,7 +41,12 @@ test: about: home: https://github.com/jeffdaily/parasail-python - license: BSD + summary: "Python bindings for the parasail C library containing implementations of pairwise sequence alignment algorithms." + license: BSD-3-Clause license_family: BSD - summary: pairwise sequence alignment library + license_file: COPYING + dev_url: https://pypi.org/project/parasail/ +extra: + identifiers: + - doi:10.1186/s12859-016-0930-z From 92dd084673673407d463583bcda4a9896df657f8 Mon Sep 17 00:00:00 2001 From: Wenbin Zhou Date: Sat, 1 Jul 2023 03:23:33 -0400 Subject: [PATCH 07/80] update ptgaul meta.yaml (#39538) Co-authored-by: Brandon Seah --- recipes/ptgaul/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/ptgaul/meta.yaml b/recipes/ptgaul/meta.yaml index 6a46713416fc39..5f91a31a85e850 100644 --- a/recipes/ptgaul/meta.yaml +++ b/recipes/ptgaul/meta.yaml @@ -11,7 +11,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: build: @@ -19,7 +19,7 @@ requirements: - seqkit - seqtk - assembly-stats - - flye + - flye 2.7-0 - python >=3 - biopython @@ -28,7 +28,7 @@ requirements: - seqkit - seqtk - assembly-stats - - flye + - flye 2.7-0 - python >=3 - biopython From fe9a00ba133a326046ee6fe36f7ff5667c4e6b60 Mon Sep 17 00:00:00 2001 From: Roger Volden <86446058+velociroger-pb@users.noreply.github.com> Date: Sat, 1 Jul 2023 00:33:04 -0700 Subject: [PATCH 08/80] Update pbfusion recipe for v0.2.2 (#41786) * Update checksum and remove gffcache * Fix URL --- recipes/pbfusion/build.sh | 3 --- recipes/pbfusion/meta.yaml | 10 +++------- 2 files changed, 3 insertions(+), 10 deletions(-) diff --git a/recipes/pbfusion/build.sh b/recipes/pbfusion/build.sh index bd4287c05cfd9a..9fdd2608168396 100644 --- a/recipes/pbfusion/build.sh +++ b/recipes/pbfusion/build.sh @@ -2,10 +2,7 @@ mkdir -p "${PREFIX}"/bin gunzip *.gz -mv gffcache* gffcache mv pbfusion* pbfusion -chmod +x gffcache chmod +x pbfusion -cp gffcache "${PREFIX}"/bin/ cp pbfusion "${PREFIX}"/bin/ diff --git a/recipes/pbfusion/meta.yaml b/recipes/pbfusion/meta.yaml index 904c901e0fa445..781ada3413aea9 100644 --- a/recipes/pbfusion/meta.yaml +++ b/recipes/pbfusion/meta.yaml @@ -1,17 +1,14 @@ {% set name = "pbfusion" %} -{% set version = "0.1.0" %} -{% set pbfusion_sha256 = "094e7b2f79b0505d62635b4c33f078f18e3a522296209aebf11ec9c194dc47c6" %} -{% set gffcache_sha256 = "d5cd010103a390d7749c59b57c6abe22312cff6b737dd322535f9e76d3ef941a" %} +{% set version = "0.2.2" %} +{% set pbfusion_sha256 = "3390adbeb8550265fcf4fad89dad80740cc368e96d10f3b23bb19ef001ffd081" %} package: name: {{ name }} version: {{ version }} source: - - url: https://github.com/PacificBiosciences/pbfusion/releases/download/v{{ version }}/pbfusion-v{{ version }}-linux_x86_64.gz + - url: https://github.com/PacificBiosciences/pbfusion/releases/download/{{ version }}/pbfusion-v{{ version }}-linux_x86_64.gz sha256: {{ pbfusion_sha256 }} - - url: https://github.com/PacificBiosciences/pbfusion/releases/download/v{{ version }}/gffcache-v{{ version }}-linux_x86_64.gz - sha256: {{ gffcache_sha256 }} about: home: https://github.com/PacificBiosciences/pbfusion @@ -31,4 +28,3 @@ build: test: commands: - pbfusion --version - - gffcache --version From 7d4e426fbf9f429ee1ae19ee51ea66d9f16ae1f6 Mon Sep 17 00:00:00 2001 From: Bernhard Reuter Date: Sat, 1 Jul 2023 09:35:36 +0200 Subject: [PATCH 09/80] Add geno2phenoTB (#41685) * Add recipe for geno2phenoTB. * Fix recipe. --- recipes/geno2phenotb/meta.yaml | 49 ++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 recipes/geno2phenotb/meta.yaml diff --git a/recipes/geno2phenotb/meta.yaml b/recipes/geno2phenotb/meta.yaml new file mode 100644 index 00000000000000..9cc9d7ecffdd0d --- /dev/null +++ b/recipes/geno2phenotb/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set sha256 = "a1c1778761992f40f15c25efb2601118d0e6c7b53c17a697a290189393bbf146" %} + +package: + name: geno2phenotb + version: "{{ version }}" + +source: + url: https://github.com/msmdev/geno2phenoTB/archive/refs/tags/{{ version }}.tar.gz + sha256: "{{ sha256 }}" + +build: + noarch: python + number: 0 + script: python -m pip install --no-deps --ignore-installed . + +requirements: + host: + - python =3.7.15 + - pip + - setuptools =65.5.0 + run: + - bwa =0.7.17 + - gatk =3.8 + - imbalanced-learn =0.8.1 + - joblib =1.1.1 + - mtbseq =1.0.4 + - numpy =1.21.5 + - numpy-base =1.21.5 + - packaging =21.3 + - pandas =0.25.3 + - perl-base =2.23 + - python =3.7.15 + - samtools =1.6 + - scikit-learn =0.24.2 + - scipy =1.7.3 + - setuptools =65.5.0 + - importlib_metadata + - wheel =0.37.1 + +test: + imports: + - geno2phenotb + +about: + home: https://github.com/msmdev/geno2phenoTB + license: LGPL-3.0-only + license_file: LICENSE.txt + summary: Machine learning based engine to predict Mycobacterium tuberculosis drug resistance using whole-genome sequencing data From 0899b7c724efee66ccc6ca0d5873f4ca83d73a1d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 01:36:13 -0600 Subject: [PATCH 10/80] Update perl-graph to 0.9727 (#41673) --- recipes/perl-graph/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-graph/meta.yaml b/recipes/perl-graph/meta.yaml index 9fb5e01a9bffe2..ae771f48d77ff3 100644 --- a/recipes/perl-graph/meta.yaml +++ b/recipes/perl-graph/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-graph - version: "0.9726" + version: "0.9727" source: - url: https://cpan.metacpan.org/authors/id/E/ET/ETJ/Graph-0.9726.tar.gz - sha256: 7a60c7746da3f2da43f4acea703be2ad8fa24b26a623a0745876020e6ecd970e + url: https://cpan.metacpan.org/authors/id/E/ET/ETJ/Graph-0.9727.tar.gz + sha256: 392a8916dc95131abe8c913dfcac7698484bf4866b42af5f7043c0062e742229 build: noarch: generic From 207f3b86a33f0e39a2ae546ef8241828fd05f62b Mon Sep 17 00:00:00 2001 From: Thanh Lee Date: Sat, 1 Jul 2023 08:39:04 +0100 Subject: [PATCH 11/80] Update meta.yaml (#41647) add missing samtools Co-authored-by: Brandon Seah --- recipes/quatradis/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml index 2116b1103c31f5..2881fed106ce83 100644 --- a/recipes/quatradis/meta.yaml +++ b/recipes/quatradis/meta.yaml @@ -9,7 +9,7 @@ source: sha256: 8ff35ebb615d6ab4698f3204d0517c432ac987cb4f570b1b0a0d2d2fadb73af4 build: - number: 0 + number: 1 script: python -m pip install -v --no-deps --ignore-installed . requirements: @@ -39,6 +39,7 @@ requirements: - r-getopt - r-mass - bwa + - samtools - minimap2 - snakemake - snakeviz From 899b1f35d2657182742f4f0f8cadad819e7796b2 Mon Sep 17 00:00:00 2001 From: Pablo Moreno Date: Sat, 1 Jul 2023 08:39:36 +0100 Subject: [PATCH 12/80] Adds decoupler python (#41651) --- recipes/decoupler/meta.yaml | 44 +++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 recipes/decoupler/meta.yaml diff --git a/recipes/decoupler/meta.yaml b/recipes/decoupler/meta.yaml new file mode 100644 index 00000000000000..5b35ee32e506d4 --- /dev/null +++ b/recipes/decoupler/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "decoupler" %} +{% set version = "1.4.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/decoupler-{{ version }}.tar.gz + sha256: ecb350a2f4717fdcfc3ad8e0e1ed3faa8214d28ff7d2f3ff90b195c91d826433 + +build: + noarch: python + script: {{ PYTHON }} -m pip install . -vv + number: 0 + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - numba + - tqdm + - anndata + - typing-extensions + +test: + imports: + - decoupler + commands: + - pip check + requires: + - pip + +about: + home: https://github.com/saezlab/decoupler-py + summary: Ensemble of methods to infer biological activities from omics data + license: GPL-3.0 + license_file: LICENSE + +extra: + recipe-maintainers: + - pcm32 From 7643d584d79e76ea659b9ee1bfc126146eb21a88 Mon Sep 17 00:00:00 2001 From: michalk8 <46717574+michalk8@users.noreply.github.com> Date: Sat, 1 Jul 2023 09:40:29 +0200 Subject: [PATCH 13/80] Remove `scVelo` (#41617) --- recipes/scvelo/meta.yaml | 48 ---------------------------------------- 1 file changed, 48 deletions(-) delete mode 100644 recipes/scvelo/meta.yaml diff --git a/recipes/scvelo/meta.yaml b/recipes/scvelo/meta.yaml deleted file mode 100644 index a0e5d2366148a1..00000000000000 --- a/recipes/scvelo/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -{% set name = "scvelo" %} -{% set version = "0.2.5" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 7e32d9e34245971330d69c12f4339cebe0acebb61e59a8b1aca9b369078b5207 - -build: - noarch: python - number: 0 - script: "{{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv" - -requirements: - host: - - pip - - python >=3.6 - - setuptools_scm - run: - - anndata >=0.7.0 - - loompy >=2.0.12 - - matplotlib-base >=3.1.2 - - numpy >=1.17 - - pandas >=0.23 - - python >=3.6 - - scanpy >=1.5.0 - - scikit-learn >=0.21.2 - - scipy >=1.4.1 - - typing_extensions - - umap-learn >=0.3.10 - -test: - imports: - - scvelo - - scvelo.pl - - scvelo.pp - - scvelo.tl - - scvelo.utils - -about: - home: "https://github.com/theislab/scvelo" - license: BSD - license_family: BSD - license_file: LICENSE - summary: "single-cell RNA velocity generalized to transient cell states" From f695944b7ecea3083ef3ed1d9e080297b2ef8abb Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:41:31 -0500 Subject: [PATCH 14/80] Update MEME to 5.5.3 (#41596) * Update MEME to 5.5.3 * do not skip building on OSX --- recipes/meme/build.sh | 30 +++++++++++++++++++---------- recipes/meme/meta.yaml | 43 ++++++++++++------------------------------ 2 files changed, 32 insertions(+), 41 deletions(-) diff --git a/recipes/meme/build.sh b/recipes/meme/build.sh index 3662778acf02fc..58e05134d1b504 100644 --- a/recipes/meme/build.sh +++ b/recipes/meme/build.sh @@ -1,14 +1,24 @@ -#!/bin/sh +#!/bin/bash set -e -MEME_ETC_DIR=${PREFIX}/etc + +export MEME_ETC_DIR=${PREFIX}/etc #HOME=/tmp cpanm CGI::Application #HOME=/tmp cpanm XML::Parser::Expat --configure-args "EXPATLIBPATH=$PREFIX/lib" --configure-args "EXPATHINCPATH=$PREFIX/include" + +autoconf +autoheader + perl scripts/dependencies.pl -./configure --prefix="${PREFIX}" --enable-build-libxml2 --enable-build-libxslt CC=${CC} +./configure CC="${CC}" \ + CFLAGS="-O3 -I${PREFIX}/include" \ + LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \ + --prefix="${PREFIX}" \ + --enable-build-libxml2 \ + --enable-build-libxslt make clean -make CC=${CC} AM_CFLAGS='-DNAN="(0.0/0.0)"' +make AM_CFLAGS='-DNAN="(0.0/0.0)"' -j4 # tests will only work inside the build dir, but # https://github.com/conda/conda-build/issues/1453 @@ -18,14 +28,14 @@ make CC=${CC} AM_CFLAGS='-DNAN="(0.0/0.0)"' make install -ln -s $PREFIX/libexec/$PKG_NAME-$PKG_VERSION/* $PREFIX/bin/ +ln -s ${PREFIX}/libexec/${PKG_NAME}-${PKG_VERSION}/* ${PREFIX}/bin/ # if building with python3, # modify meme-chip script to use python3 version of DREME -if [ $PY3K==1 ]; then - sed -i.bak '994s/dreme/dreme-py3/' $PREFIX/bin/meme-chip - rm $PREFIX/bin/meme-chip.bak - # Fix for dreme - cp scripts/*py3.py $PREFIX/lib/$PKG_NAME-$PKG_VERSION/python/ +if [ ${PY3K}==1 ]; then + sed -i.bak '994s/dreme/dreme-py3/' ${PREFIX}/bin/meme-chip + rm ${PREFIX}/bin/meme-chip.bak + # Fix for dreme + cp scripts/*py3.py ${PREFIX}/lib/${PKG_NAME}-${PKG_VERSION}/python/ fi diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index d261107dcaaeee..4157eeb981b4cf 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -1,6 +1,6 @@ {% set name = "MEME" %} -{% set version = "5.5.2" %} -{% set sha256 = "340644438dac7584895ecffafa8c1fb7de57c705a34045c1ea1bde785bab05a3" %} +{% set version = "5.5.3" %} +{% set sha256 = "203abf6d89da15f346e6cbf25795fb0659020755df54e8b4b69cb0d4e636e8a1" %} package: name: {{ name|lower }} @@ -11,19 +11,19 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 detect_binary_files_with_prefix: True requirements: build: - - make - {{ compiler('c') }} - - nodejs >=16.4.1 + - make + - autoconf host: + - nodejs >=16.4.1 - openmpi - yaml - icu - - python - ghostscript - zlib - xz @@ -31,41 +31,22 @@ requirements: - libxml2 - expat - perl - - perl-xml-parser + run: + - python >=3.7 + - perl - perl-app-cpanminus - perl-module-build - perl-yaml - - perl-xml-simple - - perl-html-template - perl-cgi - - perl-html-parser - - perl-html-tree - perl-math-cdf - perl-log-log4perl - - perl-json - - perl-file-which - - perl-sys-info - run: - - openmpi - - yaml - - icu - - expat - - python - - perl - - libxslt - - libxml2 - - ghostscript - - perl-xml-parser - - perl-yaml - perl-xml-simple - - perl-html-template - - perl-cgi + - perl-xml-parser + - perl-file-which - perl-html-parser + - perl-html-template - perl-html-tree - - perl-math-cdf - - perl-log-log4perl - perl-json - - perl-file-which - perl-sys-info test: From 8c863f013aa615fc6383b656173540103a6ac0a6 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Sat, 1 Jul 2023 16:41:50 +0900 Subject: [PATCH 15/80] cwltest has migrated to conda-forge (#41588) https://anaconda.org/conda-forge/cwltest https://github.com/conda-forge/cwltest-feedstock/ --- recipes/cwltest/meta.yaml | 40 --------------------------------------- 1 file changed, 40 deletions(-) delete mode 100644 recipes/cwltest/meta.yaml diff --git a/recipes/cwltest/meta.yaml b/recipes/cwltest/meta.yaml deleted file mode 100644 index e547c8d3a46476..00000000000000 --- a/recipes/cwltest/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set version = "2.2.20220521103021" %} - -package: - name: cwltest - version: {{ version }} - -source: - url: https://pypi.io/packages/source/c/cwltest/cwltest-{{ version }}.tar.gz - sha256: 57ff03467a150140f7ea5662e8265d016f3e75481fe047b6a3dbdfc022cbc889 - -build: - number: 0 - noarch: python - entry_points: - - cwltest=cwltest:main - - mock-cwl-runner=cwltest.tests.mock_cwl_runner:main - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv - -requirements: - host: - - pip - - python >=3.6 - run: - - junit-xml >=1.8 - - python >=3.6 - - schema-salad >=5.0.20200220195218 - - defusedxml - -test: - imports: - - cwltest - - cwltest.tests - commands: - - cwltest --help - - mock-cwl-runner --help - -about: - home: https://github.com/common-workflow-language/cwltest - license: Apache-2.0 - summary: Common workflow language testing framework From c3a98cf64845aebbdb0701ca37e6dc1faefb979d Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:42:35 -0500 Subject: [PATCH 16/80] Update sage-proteomics to 0.13.3 (#41618) * Update sage-proteomics to 0.13.2 * Update sage-proteomics to 0.13.3 --- recipes/sage-proteomics/build.sh | 10 ++++++---- recipes/sage-proteomics/meta.yaml | 14 +++++++------- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/recipes/sage-proteomics/build.sh b/recipes/sage-proteomics/build.sh index 91129d3d2c0655..0d6a1d40a31264 100644 --- a/recipes/sage-proteomics/build.sh +++ b/recipes/sage-proteomics/build.sh @@ -1,9 +1,11 @@ -#!/bin/bash +#!/bin/bash -export CFLAGS="${CFLAGS} -fcommon" -export CXXFLAGS="${CFLAGS} -fcommon" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +export CFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include ${LDFLAGS}" export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" # build statically linked binary with sage -RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path crates/sage-cli +RUST_BACKTRACE=1 cargo install --verbose -j 4 --root ${PREFIX} --path crates/sage-cli diff --git a/recipes/sage-proteomics/meta.yaml b/recipes/sage-proteomics/meta.yaml index 57188192f870a9..d5d3587f08509d 100644 --- a/recipes/sage-proteomics/meta.yaml +++ b/recipes/sage-proteomics/meta.yaml @@ -1,23 +1,23 @@ {% set name = "sage-proteomics" %} -{% set version = "0.13.1" %} +{% set version = "0.13.3" %} +{% set sha256 = "93f022efd847cf28be9fccb693f1ca9500e1001203d90dc143198186f2c3ce59" %} package: - name: {{ name|lower }} - version: {{ version }} + name: {{ name }} + version: {{ version }} build: - number: 2 + number: 0 source: url: https://github.com/lazear/sage/archive/refs/tags/v{{ version }}.tar.gz - sha256: 75ae7b0c8b96650f60a0d4fab43ae67a7ea4eb0ecc661235a7a2c34f9cbf8e8d + sha256: {{ sha256 }} requirements: build: - {{ compiler('c') }} - - rust >=1.62.0 host: - run: + - rust >=1.70.0 test: commands: From 987a926c1aa2e471aa3d88018717a0439a7f7daa Mon Sep 17 00:00:00 2001 From: Michael Hall Date: Sat, 1 Jul 2023 17:43:24 +1000 Subject: [PATCH 17/80] add skc recipe (#41579) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Johannes Köster --- recipes/skc/build.sh | 9 +++++++++ recipes/skc/meta.yaml | 32 ++++++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 recipes/skc/build.sh create mode 100644 recipes/skc/meta.yaml diff --git a/recipes/skc/build.sh b/recipes/skc/build.sh new file mode 100644 index 00000000000000..62b31a780b17bf --- /dev/null +++ b/recipes/skc/build.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -ex + +# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. +# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. +export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo" +export RUST_BACKTRACE=full + +cargo install --verbose --path . --root $PREFIX --locked \ No newline at end of file diff --git a/recipes/skc/meta.yaml b/recipes/skc/meta.yaml new file mode 100644 index 00000000000000..34248e6a791a83 --- /dev/null +++ b/recipes/skc/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "0.1.0" %} +{% set name = "skc" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/mbhall88/{{ name }}/archive/{{ version }}.tar.gz + sha256: 559362cdc16b4bd7e9cb3d6d3b619e95551b3e29cffd01929cce365a6f4f3f35 + +build: + number: 0 + +requirements: + build: + - rust >=1.65.0 + - {{ compiler('c') }} + +test: + commands: + - skc --help + +about: + home: https://github.com/mbhall88/skc + license: MIT + summary: Shared k-mer content between two genomes + license_file: LICENSE + +extra: + recipe-maintainers: + - mbhall88 \ No newline at end of file From bc54b59ac1190431db9c85e201d3771cb295d7a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 01:45:54 -0600 Subject: [PATCH 18/80] Update perl-cpan-meta-requirements to 2.143 (#41571) --- recipes/perl-cpan-meta-requirements/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-cpan-meta-requirements/meta.yaml b/recipes/perl-cpan-meta-requirements/meta.yaml index 2aceff36f940a6..8bb0f674f996c9 100644 --- a/recipes/perl-cpan-meta-requirements/meta.yaml +++ b/recipes/perl-cpan-meta-requirements/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-cpan-meta-requirements" %} -{% set version = "2.142" %} -{% set sha256 = "e0028ec7ce80905a59854f07eb17fedf7c6d16725aa72c1bb774dbfff2bdc456" %} +{% set version = "2.143" %} +{% set sha256 = "6ec7e4697bb5a8cea0ee3c8bd5d4b20ce086168a8084778d6e7a4c37356fdf8b" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/R/RJ/RJBS/CPAN-Meta-Requirements-2.142.tar.gz + url: https://cpan.metacpan.org/authors/id/R/RJ/RJBS/CPAN-Meta-Requirements-2.143.tar.gz sha256: {{ sha256 }} build: From 1d34bae5f8063a5381abaa5af84db16010da0276 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 01:46:59 -0600 Subject: [PATCH 19/80] Update pango-designation to 1.21 (#41615) --- recipes/pango-designation/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pango-designation/meta.yaml b/recipes/pango-designation/meta.yaml index 356d0802137ff8..6adba4024b6665 100644 --- a/recipes/pango-designation/meta.yaml +++ b/recipes/pango-designation/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.20" %} +{% set version = "1.21" %} package: name: pango-designation @@ -6,7 +6,7 @@ package: source: url: https://github.com/cov-lineages/pango-designation/archive/refs/tags/v{{ version }}.tar.gz - sha256: 924c7757836166ab7cbfcd10f41e54abddb67358d64dcd9f72407aadfafee56e + sha256: c0bb6cd3a01ff11d0929e8001a355bc54383bb1109d5be68585d8b5d2bca11b6 build: number: 0 From ab15bbe47394754e8f53472647cfd1818ce350da Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Sat, 1 Jul 2023 16:49:10 +0900 Subject: [PATCH 20/80] Update toil to 5.11.0 (#41533) Co-authored-by: Brandon Seah --- recipes/toil/meta.yaml | 17 +++++++++-------- recipes/toil/remove_wdlparse.patch | 15 +++++++++------ 2 files changed, 18 insertions(+), 14 deletions(-) diff --git a/recipes/toil/meta.yaml b/recipes/toil/meta.yaml index 4feca060d030c1..ae64ff3a96df13 100644 --- a/recipes/toil/meta.yaml +++ b/recipes/toil/meta.yaml @@ -1,11 +1,11 @@ -{% set version="5.9.2" %} +{% set version="5.11.0" %} package: name: toil version: {{ version }} source: url: https://pypi.io/packages/source/t/toil/toil-{{ version }}.tar.gz - sha256: 15018c0215448890c4a6ea4e4a122791bab7ab200424831c0a4eacaa57df0120 + sha256: b5565ab9251f58c06c4ae5617e4484961e6923974d0e1bc4356a61f71ec8ea19 patches: - remove_wdlparse.patch @@ -15,11 +15,11 @@ build: entry_points: - toil = toil.utils.toilMain:main - _toil_worker = toil.worker:main - - toil-cwl-runner = toil.cwl.cwltoil:main [cwl] + - toil-cwl-runner = toil.cwl.cwltoil:main #- toil-wdl-runner = toil.wdl.toilwdl:main #- toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server] - - _toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos] - #- _toil_contained_executor = toil.batchSystems.contained_executor:executor + - _toil_mesos_executor = toil.batchSystems.mesos.executor:main + - _toil_contained_executor = toil.batchSystems.contained_executor:executor requirements: host: @@ -30,6 +30,7 @@ requirements: - dill >=0.3.2,<0.4 - requests >=2,<3 - docker-py >=3.7.2,<6 + - urllib3 >=1.26.0,<2.0.0 - python-dateutil - psutil >=3.0.1,<6 #- py-tes >=0.4.2,<1 @@ -58,14 +59,14 @@ requirements: - pynacl >=1.4.0,<2 #google reqs - apache-libcloud >=2.2.1,<3 - - google-cloud-storage >=1.6.0,<2 + - google-cloud-storage >=2,<=2.8.0 #cwl reqs - - cwltool ==3.1.20221201130942 + - cwltool ==3.1.20230425144158 - schema-salad >=8.4.20230128170514,<9 - galaxy-tool-util - ruamel.yaml >=0.15,<=0.17.21 - ruamel.yaml.clib >=0.2.6 - - networkx >=2,<2.8.5 + - networkx >=2,<2.8.9 #htcondor reqs - python-htcondor >=10.2.0.post1,<11 #kubernetes reqs diff --git a/recipes/toil/remove_wdlparse.patch b/recipes/toil/remove_wdlparse.patch index 83345d9fe30f26..e2ccea7bd7c43e 100644 --- a/recipes/toil/remove_wdlparse.patch +++ b/recipes/toil/remove_wdlparse.patch @@ -1,6 +1,8 @@ ---- toil-releases-5.7.1-orig/setup.py 2022-12-09 09:21:30.676954931 +0000 -+++ toil-releases-5.7.1/setup.py 2022-12-09 09:21:44.129209710 +0000 -@@ -53,7 +53,6 @@ +diff --git a/setup.py b/setup.py +index 67c23b061..32ba9bd85 100755 +--- a/setup.py ++++ b/setup.py +@@ -54,7 +54,6 @@ def run_setup(): "google", "kubernetes", "mesos", @@ -8,11 +10,12 @@ "server" ] for extra in non_htcondor_extras: -@@ -113,8 +112,6 @@ +@@ -112,8 +111,6 @@ def run_setup(): '_toil_worker = toil.worker:main', 'cwltoil = toil.cwl.cwltoil:cwltoil_was_removed [cwl]', 'toil-cwl-runner = toil.cwl.cwltoil:main [cwl]', -- 'toil-wdl-runner = toil.wdl.toilwdl:main', -- 'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]', +- 'toil-wdl-runner = toil.wdl.wdltoil:main [wdl]', +- 'toil-wdl-runner-old = toil.wdl.toilwdl:main [wdl]', + 'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main [server]', '_toil_mesos_executor = toil.batchSystems.mesos.executor:main [mesos]', '_toil_contained_executor = toil.batchSystems.contained_executor:executor']}) From 595968723fdf483c0240f2d082caf11681e79f46 Mon Sep 17 00:00:00 2001 From: deliaBlue <103108590+deliaBlue@users.noreply.github.com> Date: Sat, 1 Jul 2023 09:57:26 +0200 Subject: [PATCH 21/80] Add oligomap software package (#41667) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add oligomap files * build: remove CMakeLists.txt * build: remove oligomap.cpp * refactor: update recipe * build: add osx dependencies * refactor: update recipe * build: update URL and sha256 * The license file is shipped with the source tarball --------- Co-authored-by: Iris Mestres Co-authored-by: Brandon Seah Co-authored-by: Björn Grüning --- recipes/oligomap/meta.yaml | 43 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/oligomap/meta.yaml diff --git a/recipes/oligomap/meta.yaml b/recipes/oligomap/meta.yaml new file mode 100644 index 00000000000000..8219cb0ada660c --- /dev/null +++ b/recipes/oligomap/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.1" %} + +package: + name: oligomap + version: {{ version }} + +source: + url: https://github.com/zavolanlab/oligomap/archive/refs/tags/v1.0.1.tar.gz + sha256: 0dba5ca4a4ed098c129a7558115d6d48bbb9ce2f0fe508e46181b017ef51eb85 + +build: + number: 0 + binary_relocation: true + script: + - cmake -H. -Bbuild_conda -G "${CMAKE_GENERATOR}" -DCMAKE_INSTALL_PREFIX=${PREFIX} + - cmake --build build_conda --target install + +requirements: + build: + - make + - {{ compiler('cxx') }} + - libtool + - automake + - cmake + - m4 + host: + - zlib + run: + - zlib + +test: + commands: + - oligomap 2>&1 | grep Usage + +about: + home: https://github.com/zavolanlab/oligomap + license: GNU Affero General Public License v3.0 + license_file: LICENSE + summary: Oligomap is a program for fast identification of nearly-perfect matches of small RNAs in sequence databases. + +extra: + identifiers: + - doi:10.1016/j.ymeth.2007.10.002 From c2cd71dc84cd637c7c615370d6177fa5e36ad832 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:00:29 -0500 Subject: [PATCH 22/80] Add recipe for WFA2-lib v2.3.3 (#41597) * Add recipe for WFA2-lib v2.3.3 * add CXX compiler flag * do not skip building on OSX * remove -ftree-vectorizer-verbose=5 * try changing LDFLAGS * fix osx test --- recipes/wfa2-lib/build.sh | 17 ++++ recipes/wfa2-lib/makefile.patch | 141 ++++++++++++++++++++++++++++++++ recipes/wfa2-lib/meta.yaml | 41 ++++++++++ 3 files changed, 199 insertions(+) create mode 100644 recipes/wfa2-lib/build.sh create mode 100644 recipes/wfa2-lib/makefile.patch create mode 100644 recipes/wfa2-lib/meta.yaml diff --git a/recipes/wfa2-lib/build.sh b/recipes/wfa2-lib/build.sh new file mode 100644 index 00000000000000..523f810bac3b2b --- /dev/null +++ b/recipes/wfa2-lib/build.sh @@ -0,0 +1,17 @@ +#!/bin/bash +set -ex + +export C_INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +cmake -S . -B build \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_C_COMPILER="${CC}" \ + -DCMAKE_CXX_FLAGS="-O3 -D_FILE_OFFSET_BITS=64 -I${PREFIX}/include ${LDFLAGS}" \ + -DEXTRA_FLAGS="-ftree-vectorize -msse2 -mfpmath=sse" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + -DBUILD_SHARED_LIBS=ON + +cmake --build build/ --target install -v diff --git a/recipes/wfa2-lib/makefile.patch b/recipes/wfa2-lib/makefile.patch new file mode 100644 index 00000000000000..30322d25a85993 --- /dev/null +++ b/recipes/wfa2-lib/makefile.patch @@ -0,0 +1,141 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ab399ba..07d6874 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -59,8 +59,8 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) + endif() + + if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo)) +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS} ${OPTIMIZE_FLAGS}") +- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} ${OPTIMIZE_FLAGS}") ++ SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPTIMIZE_FLAGS}") ++ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPTIMIZE_FLAGS}") + endif () + + if (${CMAKE_BUILD_TYPE} MATCHES "Debug") +@@ -150,6 +150,11 @@ target_include_directories(wfa2_static PUBLIC . wavefront utils) + add_library(wfa2::wfa2 ALIAS wfa2) + add_library(wfa2::wfa2_static ALIAS wfa2_static) + ++if(OPENMP) ++ target_link_libraries(wfa2_static PRIVATE OpenMP::OpenMP_C) ++ target_link_libraries(wfa2 PRIVATE OpenMP::OpenMP_C) ++endif(OPENMP) ++ + # ---- C++ binding library + + set(wfa2cpp_SOURCE +@@ -163,13 +168,18 @@ add_library(wfa2cpp SHARED ${wfa2cpp_SOURCE}) + set_target_properties(wfa2cpp PROPERTIES SOVERSION 0) + set_target_properties(wfa2cpp_static PROPERTIES OUTPUT_NAME wfa2cpp) + target_link_libraries(wfa2cpp PUBLIC wfa2) +-target_link_libraries(wfa2cpp_static PUBLIC wfa2) ++target_link_libraries(wfa2cpp_static PUBLIC wfa2_static) + add_library(wfa2::wfa2cpp ALIAS wfa2cpp) + add_library(wfa2::wfa2cpp_static ALIAS wfa2cpp_static) + ++if(OPENMP) ++ target_link_libraries(wfa2cpp_static PRIVATE OpenMP::OpenMP_CXX) ++ target_link_libraries(wfa2cpp PRIVATE OpenMP::OpenMP_CXX) ++endif(OPENMP) ++ + # ---- Get version + +-file (STRINGS "VERSION" BUILD_NUMBER) ++file (STRINGS "VERSION.txt" BUILD_NUMBER) + add_definitions(-DWFA2LIB_VERSION="${BUILD_NUMBER}") + add_definitions(-DVERSION="${BUILD_NUMBER}") + +diff --git a/Makefile b/Makefile +index 37ca094..4f0ced3 100644 +--- a/Makefile ++++ b/Makefile +@@ -12,7 +12,7 @@ UNAME=$(shell uname) + CC:=$(CC) + CPP:=$(CXX) + +-CC_FLAGS=-Wall -g ++CC_FLAGS=-Wall -g -fPIE + + AR=ar + AR_FLAGS=-rsc +diff --git a/VERSION b/VERSION.txt +similarity index 100% +rename from VERSION +rename to VERSION.txt +diff --git a/alignment/cigar.c b/alignment/cigar.c +index 4c4efe3..b79f06c 100644 +--- a/alignment/cigar.c ++++ b/alignment/cigar.c +@@ -494,10 +494,10 @@ void cigar_print_pretty( + } + // Print alignment pretty + fprintf(stream," ALIGNMENT\t"); +- cigar_print(stderr,cigar,true); ++ cigar_print(stream,cigar,true); + fprintf(stream,"\n"); + fprintf(stream," ALIGNMENT.COMPACT\t"); +- cigar_print(stderr,cigar,false); ++ cigar_print(stream,cigar,false); + fprintf(stream,"\n"); + fprintf(stream," PATTERN %s\n",pattern_alg); + fprintf(stream," %s\n",ops_alg); +diff --git a/bindings/cpp/WFAligner.hpp b/bindings/cpp/WFAligner.hpp +index 373bb2d..8da82bb 100644 +--- a/bindings/cpp/WFAligner.hpp ++++ b/bindings/cpp/WFAligner.hpp +@@ -33,6 +33,7 @@ + #define BINDINGS_CPP_WFALIGNER_HPP_ + + #include ++#include + + #include "../../wavefront/wfa.hpp" + +diff --git a/utils/commons.h b/utils/commons.h +index a1f0132..7d60243 100644 +--- a/utils/commons.h ++++ b/utils/commons.h +@@ -31,6 +31,7 @@ + + #pragma once + ++#include + #include + #include + #include +diff --git a/utils/vector.h b/utils/vector.h +index 2c5dcf0..4bd4776 100644 +--- a/utils/vector.h ++++ b/utils/vector.h +@@ -33,6 +33,8 @@ + #ifndef VECTOR_H_ + #define VECTOR_H_ + ++#include ++ + /* + * Checkers + */ +diff --git a/wavefront/wavefront_heuristic.c b/wavefront/wavefront_heuristic.c +index 51d414c..73ada3e 100644 +--- a/wavefront/wavefront_heuristic.c ++++ b/wavefront/wavefront_heuristic.c +@@ -518,6 +518,9 @@ void wavefront_heuristic_cufoff( + if (mwavefront == NULL || mwavefront->lo > mwavefront->hi) return; + // Decrease wait steps + --(wf_heuristic->steps_wait); ++ // Save lo/hi base ++ const int hi_base = mwavefront->hi; ++ const int lo_base = mwavefront->lo; + // Select heuristic (WF-Adaptive) + if (wf_heuristic->strategy & wf_heuristic_wfadaptive) { + wavefront_heuristic_wfadaptive(wf_aligner,mwavefront,false); +@@ -537,6 +540,7 @@ void wavefront_heuristic_cufoff( + wavefront_heuristic_banded_adaptive(wf_aligner,mwavefront); + } + // Check wavefront length ++ if (lo_base == mwavefront->lo && hi_base == mwavefront->hi) return; // No wavefronts pruned + if (mwavefront->lo > mwavefront->hi) mwavefront->null = true; + // DEBUG + // const int wf_length_base = hi_base-lo_base+1; diff --git a/recipes/wfa2-lib/meta.yaml b/recipes/wfa2-lib/meta.yaml new file mode 100644 index 00000000000000..99820f92ec104f --- /dev/null +++ b/recipes/wfa2-lib/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "WFA2-lib" %} +{% set version = "2.3.3" %} +{% set sha256 = "2569650cdba395f42513a4d2c9175724a736047bb7da99a162c0abdbd651698f" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/smarco/WFA2-lib/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + patches: + - makefile.patch + +build: + number: 0 + +requirements: + build: + - {{ compiler('cxx') }} + - make + - cmake + host: + - pkg-config + - rhash # [osx] + +test: + commands: + - "ls ${PREFIX}/lib/libwfa2.so.0" # [not osx] + - "ls ${PREFIX}/lib/libwfa2.0.dylib" # [osx] + +about: + home: "https://github.com/smarco/WFA2-lib" + license: MIT + license_file: LICENSE + summary: "Wavefront alignment algorithm library v2" + +extra: + identifiers: + - doi:10.1093/bioinformatics/btaa777 + - doi:10.1101/2022.04.14.488380 From 6019afb004e95e63f50e85557bc6756fe42276e5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:01:12 -0600 Subject: [PATCH 23/80] Update sorted_nearest to 0.0.39 (#41353) --- recipes/sorted_nearest/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/sorted_nearest/meta.yaml b/recipes/sorted_nearest/meta.yaml index 5f5a26d31c4402..613fe31b6243f5 100644 --- a/recipes/sorted_nearest/meta.yaml +++ b/recipes/sorted_nearest/meta.yaml @@ -1,8 +1,8 @@ {% set name = "sorted_nearest" %} -{% set version = "0.0.37" %} +{% set version = "0.0.39" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "dd3430d76e6c2aed14cda2cb0f2a5ce359007de3d2bc689474622f819f559d31" %} +{% set hash_value = "16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1" %} package: @@ -14,7 +14,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 2 + number: 0 script: python setup.py install --single-version-externally-managed --record=record.txt requirements: From 0b58a4d121eac9fdb550c81d2bf43c074233dead Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:01:25 -0600 Subject: [PATCH 24/80] Update perl-excel-writer-xlsx to 1.11 (#41374) --- recipes/perl-excel-writer-xlsx/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-excel-writer-xlsx/meta.yaml b/recipes/perl-excel-writer-xlsx/meta.yaml index e1fed712bc87e6..c66a70eac43389 100644 --- a/recipes/perl-excel-writer-xlsx/meta.yaml +++ b/recipes/perl-excel-writer-xlsx/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-excel-writer-xlsx" %} -{% set version = "1.10" %} -{% set sha256 = "e35891f4575ffd32168aa415abe595bb52e011cfb00c49fa6522da4e539a601c" %} +{% set version = "1.11" %} +{% set sha256 = "cb3300d23119c698864ef0b73c19a72cba718bfc06ed007359a5313f961cc2a0" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.10.tar.gz + url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/Excel-Writer-XLSX-1.11.tar.gz sha256: {{ sha256 }} build: From d5db0e879472ec83548548985025c8ee0af45a56 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:02:09 -0500 Subject: [PATCH 25/80] Update sra-human-scrubber to 2.1.0 (#41397) Co-authored-by: Brandon Seah --- .../sra-human-scrubber/fix_init_db_path.patch | 18 ------------------ recipes/sra-human-scrubber/meta.yaml | 9 ++++----- 2 files changed, 4 insertions(+), 23 deletions(-) delete mode 100644 recipes/sra-human-scrubber/fix_init_db_path.patch diff --git a/recipes/sra-human-scrubber/fix_init_db_path.patch b/recipes/sra-human-scrubber/fix_init_db_path.patch deleted file mode 100644 index 6b57a525894569..00000000000000 --- a/recipes/sra-human-scrubber/fix_init_db_path.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/init_db.sh b/init_db.sh -index de67e29..03a69c5 100755 ---- a/init_db.sh -+++ b/init_db.sh -@@ -1,7 +1,10 @@ - #!/bin/bash - set -eu - -+SCRUBBER_SHARE=BIOCONDA_SED_REPLACE - VERSION=$(curl "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/current/version.txt") --cd data && curl -vf "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/${VERSION}.human_filter.db" -o "${VERSION}.human_filter.db" --ln -s "${VERSION}".human_filter.db human_filter.db -+cd ${SCRUBBER_SHARE}/data && \ -+ curl -f "https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/${VERSION}.human_filter.db" -o "${VERSION}.human_filter.db" && -+ ln -s -f "${VERSION}".human_filter.db human_filter.db -+ - exit 0 - diff --git a/recipes/sra-human-scrubber/meta.yaml b/recipes/sra-human-scrubber/meta.yaml index 3fd4d9b97a8bd2..958d4702351a95 100644 --- a/recipes/sra-human-scrubber/meta.yaml +++ b/recipes/sra-human-scrubber/meta.yaml @@ -1,6 +1,6 @@ - {% set name = "sra-human-scrubber" %} -{% set version = "2.0.0" %} +{% set version = "2.1.0" %} +{% set sha256 = "55a777274c4b091d9dc137ad3fcf9a448246cd90e3f9aa5d886dae8c0d71d513" %} package: name: {{ name }} @@ -8,14 +8,13 @@ package: source: - url: https://github.com/ncbi/{{ name }}/archive/refs/tags/{{ version|replace("_", "-") }}.tar.gz - sha256: c4c9078325b01c7aa8bc0bcdee37f2b102880d66e478d19858eef1f00056d435 + sha256: {{ sha256 }} patches: - fix_scrub_path.patch - - fix_init_db_path.patch build: - noarch: generic number: 0 + noarch: generic requirements: run: From 7cb5906f5abf41e7e75875475c32e6e4e7f37b02 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:02:35 -0600 Subject: [PATCH 26/80] Update perl-mce to 1.888 (#41387) * Update perl-mce to 1.886 * Update perl-mce to 1.887 * Update perl-mce to 1.888 --- recipes/perl-mce/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-mce/meta.yaml b/recipes/perl-mce/meta.yaml index 1c4d0e4b96f732..cb067c1ad821db 100644 --- a/recipes/perl-mce/meta.yaml +++ b/recipes/perl-mce/meta.yaml @@ -1,13 +1,13 @@ {% set name = "perl-mce" %} -{% set version = "1.884" %} -{% set sha256 = "c830c0e548094f19c620049e744258be2c121d4a86cf7c94a37599ad016daf33" %} +{% set version = "1.888" %} +{% set sha256 = "4ae8b9394c938df867c614391d0ece82ad00ddcd274a42b97409ccfd1a923be5" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.884.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MA/MARIOROY/MCE-1.888.tar.gz sha256: {{ sha256 }} build: From 58d2b1de92702bc2d598799feb9ce80da21cb8d4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:08:04 -0600 Subject: [PATCH 27/80] Update perl-datetime-locale to 1.39 (#41365) --- recipes/perl-datetime-locale/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/perl-datetime-locale/meta.yaml b/recipes/perl-datetime-locale/meta.yaml index a8e160569e76df..081669f5ecf71b 100644 --- a/recipes/perl-datetime-locale/meta.yaml +++ b/recipes/perl-datetime-locale/meta.yaml @@ -1,17 +1,17 @@ {% set name = "perl-datetime-locale" %} -{% set version = "1.38" %} -{% set sha256 = "dd7f6d358279d1df0ea7d78b9127690435246cdf46867500e9888016f9d4c867" %} +{% set version = "1.39" %} +{% set sha256 = "10c145a6c7daf7118864e97482b4ae9f94f93b9414212eee8aa30b16a8135100" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.38.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.39.tar.gz sha256: {{ sha256 }} build: - number: 1 + number: 0 requirements: build: - make From 67846975941120c89b63a8a31df68ea2ede59e3b Mon Sep 17 00:00:00 2001 From: DAWells <49305334+DAWells@users.noreply.github.com> Date: Sat, 1 Jul 2023 09:09:08 +0100 Subject: [PATCH 28/80] Add HLAfreq recipe (#41532) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * HLAfreq meta.yaml made by skeleton * set "noarch" and change matplotlib to matplotlib-base * Specify python >= 3.8 * Only pip and python in host requirements Co-authored-by: Björn Grüning * Add arviz to recipe * HLAfreq 0.0.2, require pymc >=3 * Test import HLAfreq_pymc This should confirm that pymc and arviz are installed --------- Co-authored-by: Björn Grüning --- recipes/hlafreq/meta.yaml | 46 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/hlafreq/meta.yaml diff --git a/recipes/hlafreq/meta.yaml b/recipes/hlafreq/meta.yaml new file mode 100644 index 00000000000000..ad13a124afa23a --- /dev/null +++ b/recipes/hlafreq/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "HLAfreq" %} +{% set version = "0.0.2" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: e43d70a876a6a245ecc2d6117947c5e1f6bce5824738a4d86dfecbe6c53e07f7 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . -vv" + +requirements: + host: + - python >=3.8 + - pip + run: + - bs4 + - matplotlib-base + - numpy + - pandas + - pymc >=3 + - arviz + - python >=3.8 + - requests + - scipy + +test: + imports: + - HLAfreq + - HLAfreq.HLAfreq_pymc + +about: + home: "https://github.com/Vaccitech/HLAfreq" + license: MIT + license_family: MIT + license_file: LICENSE + summary: "Download and combine HLA frequency data from multiple studies" + +extra: + recipe-maintainers: + - DAWells From 48156db94a1110eb5bdeed65839d4a8772a856a4 Mon Sep 17 00:00:00 2001 From: Clemens Schmid Date: Sat, 1 Jul 2023 10:11:32 +0200 Subject: [PATCH 29/80] update poseidon-trident to v1.2.0.0 (#41531) --- recipes/poseidon-trident/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/poseidon-trident/meta.yaml b/recipes/poseidon-trident/meta.yaml index 0e891b33da0760..d6a03cd6b45cbf 100644 --- a/recipes/poseidon-trident/meta.yaml +++ b/recipes/poseidon-trident/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.1.11.0" %} +{% set version = "1.2.0.0" %} package: name: poseidon-trident version: {{ version }} source: - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-conda-linux # [linux] - md5: 55fe1496e43c72569205b0ecac29ec2e # [linux] + md5: ff05175059360f84ea26cb7faa2da416 # [linux] - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS # [osx] - md5: d4335ab63e83f4e8e35d704504a296ef # [osx] + md5: 87054464317f891fe7c0c0e0e9665181 # [osx] build: - number: 2 + number: 0 script: - "mkdir -p $PREFIX/bin" - "mv trident* $PREFIX/bin/trident" @@ -32,6 +32,6 @@ test: - trident --version about: - home: https://poseidon-framework.github.io/#/ + home: https://www.poseidon-adna.org/#/ license: MIT summary: "A tool (trident) to work with modular genotype databases formatted using Poseidon." From 83567f702ecc79e0773b3b38c477d523c2377e08 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 1 Jul 2023 10:14:58 +0200 Subject: [PATCH 30/80] Add MZmine (#40700) * mzmie using gradlew * update to 3.4.27 - using mzmine with included JVM (since conda does not have OpenJDK 20 at the moment) * switch to building again * try jdk 20 * bump * try from branch * debug: list toolchains * try to loosen vendor requirement * add test wo grep * --enable-preview * try wo run requirements * try just gradlew * try to exclude test only * add stacktrace * also add debug * try to get jpackage running with rpm * readd openjdk runtime requirement * try to patch executable * fini ? * implement build change as patch * add extended base image needed for missing libGL.so.1 * bump to 3.6.0 * update patch * toward working tetst * fix version output * fix grep * try pipe stderr * Update recipes/mzmine/meta.yaml --- recipes/mzmine/build.patch | 28 +++++++++++++++++++++++ recipes/mzmine/build.sh | 18 +++++++++++++++ recipes/mzmine/meta.yaml | 46 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 recipes/mzmine/build.patch create mode 100644 recipes/mzmine/build.sh create mode 100644 recipes/mzmine/meta.yaml diff --git a/recipes/mzmine/build.patch b/recipes/mzmine/build.patch new file mode 100644 index 00000000000000..dcfd2832aa3ff1 --- /dev/null +++ b/recipes/mzmine/build.patch @@ -0,0 +1,28 @@ +# - without installerType set jpackage tries to create rpm and deb +# we don't need any of them, but I did not find a way to disable +# both. so we leave rpm which is available in conda (spkg isn't) +diff -ruN mzmine3-3.6.0-org/build.gradle mzmine3-3.6.0/build.gradle +--- mzmine3-3.6.0-org/build.gradle 2023-06-21 14:39:23.000000000 +0200 ++++ mzmine3-3.6.0/build.gradle 2023-06-22 17:53:22.239977816 +0200 +@@ -392,7 +392,7 @@ + if (OperatingSystem.current().isLinux()) { + // leave installer type empty to generate all that match + // for rpm, rpmbuild and rpm tools need to be installed, installerType needs to be set to "rpm" +- // installerType = "deb" ++ installerType = "rpm" + // additional options for jpackage + imageOptions = ["--icon", "src/main/resources/MZmineIcon.png"] + installerOptions = ["--linux-shortcut", +# version is set wrong https://github.com/mzmine/mzmine3/issues/1405 +diff -ruN mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties mzmine3-3.6.0/src/main/resources/mzmineversion.properties +--- mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties 2023-06-21 14:39:23.000000000 +0200 ++++ mzmine3-3.6.0/src/main/resources/mzmineversion.properties 2023-06-22 19:14:12.455764423 +0200 +@@ -3,6 +3,6 @@ + version.buildmeta= + version.major=3 + version.minor=6 +-version.patch=1 ++version.patch=0 + version.prerelease= +-version.semver=3.6.1 ++version.semver=3.6.0 diff --git a/recipes/mzmine/build.sh b/recipes/mzmine/build.sh new file mode 100644 index 00000000000000..c5ff763377fca3 --- /dev/null +++ b/recipes/mzmine/build.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +set -ex + +# debug: show available tool chains +./gradlew -q javaToolchains +./gradlew --debug --stacktrace --exclude-task test + +mkdir -p "$PREFIX" +cp -rv build/install/MZmine/* "$PREFIX" + +# for those the don't like capital letters in commands +ln -fs "$PREFIX"/bin/MZmine "$PREFIX"/bin/mzmine + +# MZmine does not run without --enable-preview +# .. so we sneek in in the command line +sed -i -e 's/exec "$JAVACMD" "$@"/exec "$JAVACMD" --enable-preview "$@"/' "$PREFIX"/bin/MZmine + diff --git a/recipes/mzmine/meta.yaml b/recipes/mzmine/meta.yaml new file mode 100644 index 00000000000000..74db59cb8c9e1c --- /dev/null +++ b/recipes/mzmine/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.6.0" %} + +package: + name: mzmine + version: {{ version }} + +build: + number: 0 + noarch: generic + +source: + - url: https://github.com/mzmine/mzmine3/archive/refs/tags/v{{ version }}.tar.gz + sha256: 0446c3e9c0fa777904fcb1354a57aaf611ef5718042930fd8c243c9245157ef2 + patches: + - "build.patch" + +requirements: + build: + - openjdk =20 + - rpm-tools + + run: + - openjdk =20 + - pango # /home/conda/.openjfx/cache/16/libjavafx_font_pango.so: libpangoft2-1.0.so.0: cannot open shared object file + +test: + commands: + - MZmine --help + - MZmine --help |& grep "Starting MZmine {{ version }}" + - MZmine --version + - MZmine --version |& grep " MZmine version:{{ version }}" +about: + home: http://mzmine.github.io/ + license: MIT + summary: Integrative analysis of multimodal mass spectrometry data + description: | + MZmine 3 is an open-source and platform-independent software for mass + spectrometry (MS) data processing and visualization. It enables large-scale + metabolomics and lipidomics research by spectral preprocessing, feature + detection, and various options for compound identification, including + spectral library querying and creation. + +extra: + # needed for libGL.so + container: + extended-base: true From dbed973d882addbb6e8e1471c1e1f69a354d2149 Mon Sep 17 00:00:00 2001 From: Yanhai Gong Date: Sat, 1 Jul 2023 16:15:16 +0800 Subject: [PATCH 31/80] Add Python-MonVar recipe (#41645) --- recipes/python-monovar/build.sh | 6 ++++++ recipes/python-monovar/meta.yaml | 36 ++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 recipes/python-monovar/build.sh create mode 100644 recipes/python-monovar/meta.yaml diff --git a/recipes/python-monovar/build.sh b/recipes/python-monovar/build.sh new file mode 100644 index 00000000000000..ed82b479e0f1a7 --- /dev/null +++ b/recipes/python-monovar/build.sh @@ -0,0 +1,6 @@ +#!/bin/sh + +mkdir -p ${PREFIX}/bin +mkdir -p ${PREFIX}/lib +cp -r ${SRC_DIR}/src/ $PREFIX/lib/monovar +ln -s $PREFIX/lib/monovar/monovar.py $PREFIX/bin/monovar.py diff --git a/recipes/python-monovar/meta.yaml b/recipes/python-monovar/meta.yaml new file mode 100644 index 00000000000000..bbe57c6fd3ae31 --- /dev/null +++ b/recipes/python-monovar/meta.yaml @@ -0,0 +1,36 @@ +{% set name = "Python-MonoVar" %} +{% set version = "0.1" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/gongyh/MonoVar/archive/refs/tags/v{{ version }}.tar.gz + sha256: b95bfe33afcf98649d4a19d291ef3b00f43b3884280b5c373a17e770a3a0d105 + +build: + noarch: generic + number: 0 + +requirements: + run: + - python + - numpy + - scipy + - pysam + - samtools + +test: + commands: + - monovar.py --version + +about: + home: https://kgithub.com/gongyh/MonoVar + license: MIT + summary: 'single cell joint genotyper, patched version' + +extra: + identifiers: + - biotools:Monovar + - doi:10.1038/nmeth.3835 From ea3dc25903757dddb84fc5d9d7d4615856ef4176 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:15:24 -0500 Subject: [PATCH 32/80] Update GMAP to 2023-06-01 (#41512) Co-authored-by: Joshua Zhuang <71105179+joshuazhuang7@users.noreply.github.com> --- recipes/gmap/build.sh | 19 +++++++++++++------ recipes/gmap/meta.yaml | 6 +++--- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/recipes/gmap/build.sh b/recipes/gmap/build.sh index d2d3ce2242c124..1c29251e70c86a 100644 --- a/recipes/gmap/build.sh +++ b/recipes/gmap/build.sh @@ -1,14 +1,15 @@ -#!/bin/sh +#!/bin/bash -export C_INCLUDE_PATH=${PREFIX}/include +export INCLUDE_PATH=${PREFIX}/include export LIBRARY_PATH=${PREFIX}/lib export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="${CFLAGS} -I${PREFIX}/include -I${BUILD_PREFIX}/include" -export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include -I${BUILD_PREFIX}/include" +export CFLAGS="${CFLAGS} -O3" +export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" if [ "$(uname)" == "Darwin" ]; then # for Mac OSX export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" + export CFLAGS="${CFLAGS} -m64" fi export LANGUAGE=en_US.UTF-8 @@ -17,7 +18,13 @@ export LC_ALL=en_US.UTF-8 autoconf autoheader -./configure CC=${CC} --prefix="${PREFIX}" --with-simd-level=sse42 -make CC=${CC} CFLAGS="${CFLAGS} ${LDFLAGS}" CPPFLAGS="${CPPFLAGS} ${LDFLAGS}" -j 4 +./configure CC=${CC} CFLAGS="${CFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + --prefix="${PREFIX}" \ + --with-gmapdb="${PREFIX}/share" \ + --with-simd-level=sse42 + +make -j4 make install make clean diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 7075d9602583db..a886b055e593ca 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2023.04.28" %} -{% set sha256 = "6e73fab2e8043ebf735c43fe8460d2abd7c1398d1e796dc5b22ba68717f4160c" %} +{% set version = "2023.06.01" %} +{% set sha256 = "c7e6f6cf644e6f66f9f5a0811a49da8cc81f095a4bd7b7cef2ab10aa5b314430" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 1 + number: 0 ignore_run_exports: - perl - perl-file-util From df63c4640380e11756c4755277338638cfa24a12 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 1 Jul 2023 10:17:46 +0200 Subject: [PATCH 33/80] initial commit of deepfplearn (#40664) * initial commit of deepfplearn * try to add more thorough tests * debug * inlcude more test data * comment tests --- recipes/deepfplearn/meta.yaml | 52 +++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/deepfplearn/meta.yaml diff --git a/recipes/deepfplearn/meta.yaml b/recipes/deepfplearn/meta.yaml new file mode 100644 index 00000000000000..2db5b6fb1b450f --- /dev/null +++ b/recipes/deepfplearn/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "deepFPlearn" %} +{% set version = "1.2" %} + +package: + name: {{ name | lower }} + version: {{ version }} + +source: + url: https://github.com/yigbt/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 1f62b049c0ae51631f9eff718c53342fbaf5ccc400ee0f87d2dc1b2304e4e816 + +build: + number: 0 + noarch: python + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + +requirements: + host: + - python >=3 + - pip + run: + # - cudatoolkit + - jsonpickle =2.1 + - matplotlib-base =3.5 + - numpy =1.22 + - pandas =1.4 + - rdkit =2022.03 + - scikit-learn =1.0 + - keras =2.9 + - tensorflow-base + # - tensorflow-gpu =2 + - wandb =0.12 + +test: +# source_files: +# - example/ + imports: + - tensorflow + - dfpl + commands: + - dfpl --help + - ls +# commenting the actual tests due to https://github.com/bioconda/bioconda-utils/issues/897 +# - dfpl train -f example/train.json +# - dfpl predict -f example/predict.json + +about: + home: https://github.com/yigbt/deepFPlearn + license: GPL + license_file: LICENSE.pdf + summary: Link molecular structures of chemicals (in form of topological fingerprints) with multiple targets. + From a54c522db96e302ec02bb95266495ba7d759305e Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:17:58 -0500 Subject: [PATCH 34/80] Update pyspoa to 0.0.9 (#41451) * Update pyspoa to 0.0.9 * add build.sh * add -O3 optimization * remove unecessary spoa patch --- recipes/pyspoa/build.sh | 9 +++++++-- recipes/pyspoa/meta.yaml | 29 +++++++++++++++++------------ 2 files changed, 24 insertions(+), 14 deletions(-) diff --git a/recipes/pyspoa/build.sh b/recipes/pyspoa/build.sh index 5caa7778fac867..c70084521ee9f6 100644 --- a/recipes/pyspoa/build.sh +++ b/recipes/pyspoa/build.sh @@ -1,4 +1,9 @@ #!/bin/bash -make build -$PYTHON -m pip install . --no-deps --ignore-install -vv +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" + +make CXX="${CXX}" \ + CXXFLAGS="${CXXFLAGS} -O3" \ + INCLUDES="-I${PREFIX}/include" \ + LIBPATH="-L${PREFIX}/lib" -j4 build +${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-install -vv diff --git a/recipes/pyspoa/meta.yaml b/recipes/pyspoa/meta.yaml index 47b8fc4641f2d1..df7591ff543ee8 100644 --- a/recipes/pyspoa/meta.yaml +++ b/recipes/pyspoa/meta.yaml @@ -1,28 +1,34 @@ {% set name = "pyspoa" %} -{% set version = "0.0.3" %} +{% set version = "0.0.9" %} +{% set sha256 = "30b883b8dfc2355a6062f9f848e825f7ffac169657190d797cf17b4314d588fe" %} package: - name: "{{ name|lower }}" - version: "{{ version }}" + name: {{ name }} + version: {{ version }} source: - url: https://github.com/nanoporetech/pyspoa/releases/download/v{{ version }}/pyspoa-{{ version }}.tar.gz - sha256: 1d5779c2d5053571fc7ce526676b79c537915ec6ad26dfed443621f90b261efa +- url: https://github.com/nanoporetech/pyspoa/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} +- url: https://github.com/rvaser/spoa/archive/refs/tags/4.0.8.tar.gz + sha256: 3fc7e837b1052bd470924e37e0ed9531e7c839cd14b400573171d3d46d3ed9cd + folder: src build: - number: 6 - skip: True # [py2k] + number: 0 + skip: True # [py < 38] requirements: build: - - make - - {{ compiler('c') }} - {{ compiler('cxx') }} + - make - cmake host: - - pybind11 - python - pip + - setuptools + - wheel + - pybind11 + - scikit-build run: - python @@ -32,8 +38,7 @@ test: about: home: https://github.com/nanoporetech/pyspoa - license: MIT License - license_family: OTHER + license: MIT license_file: LICENSE summary: Python binding to spoa library. doc_url: https://github.com/nanoporetech/spoa From 8b1e59d517adbbab07d72c6888286d2ea49c4f67 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Sat, 1 Jul 2023 03:34:44 -0500 Subject: [PATCH 35/80] Update meryl to 1.4 (#41766) * Update meryl to 1.4 * add lint skips in extras section * add license back to recipe_dir * try building from source --- recipes/meryl/0002-macos-cmath.patch | 6 +- recipes/meryl/README.licenses | 30 +++++++ recipes/meryl/build.sh | 12 ++- recipes/meryl/build_failure.osx-64.yaml | 104 ------------------------ recipes/meryl/meta.yaml | 36 ++++---- 5 files changed, 57 insertions(+), 131 deletions(-) create mode 100644 recipes/meryl/README.licenses delete mode 100644 recipes/meryl/build_failure.osx-64.yaml diff --git a/recipes/meryl/0002-macos-cmath.patch b/recipes/meryl/0002-macos-cmath.patch index efe1f5e878dae7..58469c25c66f4b 100644 --- a/recipes/meryl/0002-macos-cmath.patch +++ b/recipes/meryl/0002-macos-cmath.patch @@ -1,7 +1,7 @@ -diff --git a/src/utility/src/utility/types.H b/src/utility/src/utility/types.H +diff --git a/src/utility/src/datastructures/types-v1.H b/src/utility/src/datastructures/types-v1.H index 82ce17c..15451f4 100644 ---- a/src/utility/src/utility/types.H -+++ b/src/utility/src/utility/types.H +--- a/src/utility/src/datastructures/types-v1.H ++++ b/src/utility/src/datastructures/types-v1.H @@ -56,6 +56,7 @@ #include diff --git a/recipes/meryl/README.licenses b/recipes/meryl/README.licenses new file mode 100644 index 00000000000000..fdd8c578dc4afe --- /dev/null +++ b/recipes/meryl/README.licenses @@ -0,0 +1,30 @@ + +This software constitutes a joint work and the contributions of individual +authors are subject to different licenses. Contributions and licenses are +listed in the applicable source files, with specific details on each +individual contribution captured in the revision control system. + +-- +For all code, except as indicated otherwise: + + PUBLIC DOMAIN NOTICE + + This software is "United States Government Work" under the terms of the + United States Copyright Act. It was written as part of the authors' + official duties for the United States Government and thus cannot be + copyrighted. This software is freely available to the public for use + without a copyright notice. Restrictions cannot be placed on its present or + future use. + + Although all reasonable efforts have been taken to ensure the accuracy and + reliability of the software and associated data, the National Human Genome + Research Institute (NHGRI), National Institutes of Health (NIH) and the + U.S. Government do not and cannot warrant the performance or results that + may be obtained by using this software or data. NHGRI, NIH and the + U.S. Government disclaim all warranties as to performance, merchantability + or fitness for any particular purpose. + + Please cite the authors in any work or product based on this material. + +-- +Additional notices can be found in src/utility/README.licenses. diff --git a/recipes/meryl/build.sh b/recipes/meryl/build.sh index f1208eb67ac292..5a69fa2ff40652 100644 --- a/recipes/meryl/build.sh +++ b/recipes/meryl/build.sh @@ -1,9 +1,7 @@ #!/bin/bash -make -C src \ - BUILD_DIR="$( pwd )/build" \ - TARGET_DIR="${PREFIX}" \ - CC="${CC}" \ - CXX="${CXX}" - -rm "${PREFIX}/lib/libmeryl.a" +make -C src BUILD_DIR="$(pwd)" \ + TARGET_DIR="${PREFIX}" \ + CXX="${CXX}" \ + CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \ + LDFLAGS="${LDFLAGS} -fopenmp -L${PREFIX}/lib" -j"${CPU_COUNT}" diff --git a/recipes/meryl/build_failure.osx-64.yaml b/recipes/meryl/build_failure.osx-64.yaml deleted file mode 100644 index b854e3d3334cc9..00000000000000 --- a/recipes/meryl/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: fd46ba5de5a11de3a74a54ec742fd1020fe3ecdb1977b645f6b9226be46032b9 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - R :: Reversible A :: Applicable - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - make: Entering directory '$SRC_DIR/src' - Building release v1.3 - For 'Darwin' '21.6.0' as 'amd64' into '$PREFIX/{bin,obj}'. - Using '$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang' version '15.0.7'. - Using user-supplied CXXFLAGS '-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix'. - - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/edlib.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/edlib.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/files.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/files.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/files-buffered.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/files-buffered.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/files-compressed.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/files-compressed.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/files-memoryMapped.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/files-memoryMapped.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/logging.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/logging.C - utility/src/utility/logging.C:170:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source] - snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n", - ^ - 1 warning generated. - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/strings.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/strings.C - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/lib/libmeryl.a/utility/src/utility/system.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/meryl-1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Imeryl -Iutility utility/src/utility/system.C - utility/src/utility/system.C:167:32: error: use of undeclared identifier '_SC_PHYS_PAGES' - uint64 physPages = sysconf(_SC_PHYS_PAGES); - ^ - 1 error generated. - make: *** [Makefile:674: /opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/work/build/lib/libmeryl.a/utility/src/utility/system.o] Error 1 - make: Leaving directory '$SRC_DIR/src' - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/meryl_1685393873268/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/meryl/meta.yaml b/recipes/meryl/meta.yaml index a0900ea8423c73..9bc19a372ea8c2 100644 --- a/recipes/meryl/meta.yaml +++ b/recipes/meryl/meta.yaml @@ -1,6 +1,6 @@ {% set name = "meryl" %} -{% set version = "1.3" %} -{% set sha256 = "8872795e23513e01859e9007af74b14fee48f0d450c78e88df135da31dc79ba4" %} +{% set version = "1.4" %} +{% set sha256 = "2ca6df788cda26521c2b3672fa2d6562a6b3b57e95003cff31df596be289c92f" %} package: name: {{ name }} @@ -11,34 +11,36 @@ source: sha256: {{ sha256 }} patches: - 0001-Do-not-bail-out-for-Clang-on-macOS.patch - - 0002-macos-cmath.patch # [osx] + - 0002-macos-cmath.patch # [osx] build: - number: 2 + number: 0 requirements: build: - - make - - {{ compiler('c') }} - {{ compiler('cxx') }} - - llvm-openmp # [osx] - - libgomp # [linux] + - make host: + - llvm-openmp # [osx] + - libgomp # [linux] test: commands: - - "meryl 2>&1 | grep 'usage: meryl'" - - "meryl-analyze 2>&1 | grep 'usage: meryl-analyze'" - - "meryl-import 2>&1 | grep 'usage: meryl-import'" - - "meryl-lookup 2>&1 | grep 'usage: meryl-lookup'" - - "meryl-simple 2>&1 | grep 'usage: meryl-simple'" + - 'meryl 2>&1 | grep "usage: meryl"' + - 'meryl-analyze 2>&1 | grep "usage: meryl-analyze"' + - 'meryl-import 2>&1 | grep "usage: meryl-import"' + - 'meryl-lookup 2>&1 | grep "usage: meryl-lookup"' + - 'meryl-simple 2>&1 | grep "usage: meryl-simple"' about: home: https://github.com/marbl/meryl dev_url: https://github.com/marbl/meryl doc_url: https://github.com/marbl/meryl summary: "meryl is a multi-threaded, multi-process, out-of-core k-mer counter" - license: LicenseRef-Public-Domain AND MIT AND RSA-MD AND BSD-3-Clause AND BSD-2-Clause AND LicenseRef-parasail - license_file: - - README.licenses - - src/utility/README.licenses + license: 'Public Domain' + +extra: + identifiers: + - biotools:meryl + - usegalaxy-eu:meryl + - doi:10.1186/s13059-020-02134-9 From 12cd2ea9d2f9b5fef8d39ae64bcc886a8fb3cb91 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Sat, 1 Jul 2023 10:53:21 +0200 Subject: [PATCH 36/80] add galaxy-files (#41700) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add galaxy-files * fix lint * update version * fix link * change to LICENSE.txt --------- Co-authored-by: Björn Grüning --- recipes/galaxy-files/meta.yaml | 46 ++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 recipes/galaxy-files/meta.yaml diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml new file mode 100644 index 00000000000000..79e4dc41526a7b --- /dev/null +++ b/recipes/galaxy-files/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "23.0.4" %} +{% set sha256 = "e57f9b791d01cb2670c531d8ba7285bcb5b6595652f518b6f5be719be69243d9" %} +{% set galaxy_version = version.split(".")[:2]|join(".") %} + +package: + name: galaxy-files + version: {{ version }} + +source: + url: https://pypi.io/packages/source/g/galaxy-files/galaxy-files-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + noarch: python + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps -vv" + +requirements: + host: + - pip + - python >=3.7 + run: + - galaxy-util >={{ galaxy_version }} + - fs + - typing-extensions + - python >=3.7 + +test: + imports: + - galaxy + - galaxy.files + +about: + home: https://galaxyproject.org + license: AFL-3.0 + license_file: LICENSE.txt + summary: The Galaxy file sources framework and default plugins. + doc_url: https://docs.galaxyproject.org + dev_url: https://github.com/galaxyproject/galaxy + +extra: + identifiers: + - biotools:galaxy + - doi:10.1093/nar/gky379 + recipe-maintainers: + - bernt-matthias From 81d16521d6bfa1f5730af84ba92ad65fda079fb7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 02:56:34 -0600 Subject: [PATCH 37/80] Update peglit to 1.1.0 (#41791) --- recipes/peglit/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/peglit/meta.yaml b/recipes/peglit/meta.yaml index da1e930d8f0c3e..eb719ba9bf559c 100644 --- a/recipes/peglit/meta.yaml +++ b/recipes/peglit/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.2" %} +{% set version = "1.1.0" %} package: name: peglit @@ -6,7 +6,7 @@ package: source: url: https://github.com/sshen8/peglit/archive/refs/tags/{{ version }}.tar.gz - sha256: 06abaa273a020d461181a6cbbf0980742689619867153068d20a0457c146c833 + sha256: 06f3fae684f264f3dcf3ecd18dbadd57ca78934a07c8d8e0f68860ff05ba1754 build: number: 0 From 947fd3c5a9e69ea8e7f3725f81aae1f8914cf481 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 04:11:57 -0600 Subject: [PATCH 38/80] Update learnmsa to 1.2.4 (#41558) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update learnmsa to 1.2.0 * Update learnmsa to 1.2.1 * Update learnmsa to 1.2.3 * Update learnmsa to 1.2.4 --------- Co-authored-by: Björn Grüning --- recipes/learnmsa/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/learnmsa/meta.yaml b/recipes/learnmsa/meta.yaml index 0e9ec17c2e11c5..5a1b187d996489 100644 --- a/recipes/learnmsa/meta.yaml +++ b/recipes/learnmsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "learnMSA" %} -{% set version = "1.1.2" %} +{% set version = "1.2.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: b6b7362c967008d1dc2ed07045f05558ca2e6c1387c06054f75230a53f2b3ab2 + sha256: 96d83ea0d742e2a498ed9ce02adfdd657ae04204140555381ac8c591917fdb79 build: number: 0 From f11c96cfdb03e3f6023a40a7e25283e6785de0f0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 05:18:11 -0600 Subject: [PATCH 39/80] Update hybran to 1.7.1 (#41792) Co-authored-by: Dr. K. D. Murray <1560490+kdm9@users.noreply.github.com> --- recipes/hybran/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hybran/meta.yaml b/recipes/hybran/meta.yaml index c4e209763b6ed6..5b4b6abd054461 100644 --- a/recipes/hybran/meta.yaml +++ b/recipes/hybran/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.7" %} +{% set version = "1.7.1" %} package: name: hybran @@ -6,7 +6,7 @@ package: source: url: https://gitlab.com/LPCDRP/hybran/-/archive/{{ version }}/hybran-{{ version }}.tar.gz - sha256: '3d963b3ea258107e39c3e04b5ea06b0e79200314cecfbc0224155912df4424f5' + sha256: 'c256e88009d0a2cc3fffcb021613392f6a71ee6905bfe1a1d806b962b5243017' build: noarch: python From b9f6a26c083067def80f6b4264dc247ebeaa6b13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Sj=C3=B6din?= Date: Sat, 1 Jul 2023 13:19:49 +0200 Subject: [PATCH 40/80] Add Nanometa Live (#41744) * Add Nanometa Live * Update license to SPDX --- recipes/nanometa-live/meta.yaml | 52 +++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 recipes/nanometa-live/meta.yaml diff --git a/recipes/nanometa-live/meta.yaml b/recipes/nanometa-live/meta.yaml new file mode 100644 index 00000000000000..9cba69039c9b2f --- /dev/null +++ b/recipes/nanometa-live/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "nanometa-live" %} +{% set version = "0.1.1" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: https://github.com/FOI-Bioinformatics/nanometa_live/archive/{{ version }}.tar.gz + sha256: 59ace88e5f38531ac31137642478c5dee12f0f84b25579f5c34b009e9566e8ee + +build: + number: 0 + entry_points: + - nanometa-sim=nanometa_live.nanopore_simulator:nano_sim + - nanometa-new=nanometa_live.create_new_project:create_new + - nanometa-blastdb=nanometa_live.build_blast_db:build_blast + - nanometa-pipe=nanometa_live.nanometa_backend:check_help + - nanometa = nanometa_live.nanometa_gui:run_app + script: python -m pip install --no-deps --ignore-installed . + noarch: python + +requirements: + host: + - pip + - python >3 + + run: + - python >3 + - dash >=2.8.1 + - dash-daq >=0.5.0 + - dash-bootstrap-components >=1.3.1 + - plotly >=5.13.0 + - numpy >=1.24.1 + - pandas >=1.5.3 + - pyyaml >=6.0 + - snakemake >=7.20.0 + - blast >=2.13.0 +test: + commands: + - nanometa --help + - nanometa-sim --help + - nanometa-new --help + - nanometa-blastdb --help + - nanometa-pipe --help + +about: + home: https://github.com/FOI-Bioinformatics/nanometa_live + license: GPL-3.0-or-later + license_family: GPL3 + license_file: LICENSE.txt + summary: Workflow and GUI for real-time species classification and pathogen characterization of nanopore sequence reads. From b9e6ea8739a8470df014218fc7c632264dd63dfd Mon Sep 17 00:00:00 2001 From: Brandon Seah Date: Sat, 1 Jul 2023 14:14:28 +0200 Subject: [PATCH 41/80] Update fasta3 to v38.3.8i (#41796) Also update homepage URL --- recipes/fasta3/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/fasta3/meta.yaml b/recipes/fasta3/meta.yaml index bc1d0e24e707b6..46874424c5e50b 100644 --- a/recipes/fasta3/meta.yaml +++ b/recipes/fasta3/meta.yaml @@ -1,16 +1,16 @@ {% set name = "fasta3" %} -{% set version = "36.3.8h" %} +{% set version = "36.3.8i" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://github.com/wrpearson/fasta36/archive/refs/tags/v{{ version }}_04-May-2020.tar.gz - sha256: d13ec06a040e4d77bf6913af44b705d3ecc921131da018e71d24daf47d3664d3 + url: https://github.com/wrpearson/fasta36/archive/refs/tags/v{{ version }}_14-Nov-2020.tar.gz + sha256: b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008 build: - number: 2 + number: 0 requirements: build: @@ -35,7 +35,7 @@ test: - tfasty36 > /dev/null about: - home: http://faculty.virginia.edu/wrpearson/fasta + home: https://fasta.bioch.virginia.edu/wrpearson/fasta/ license: Apache 2.0 summary: The FASTA package - protein and DNA sequence similarity searching and alignment programs license_file: LICENSE From af2e031567bb725e38d5e03d7796ca1efaf9e5b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 08:08:07 -0600 Subject: [PATCH 42/80] Update nanoplot to 1.41.6 (#41795) --- recipes/nanoplot/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/nanoplot/meta.yaml b/recipes/nanoplot/meta.yaml index bbb29f6f21341c..ca2e5abb6cf6d6 100644 --- a/recipes/nanoplot/meta.yaml +++ b/recipes/nanoplot/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.41.3" %} +{% set version = "1.41.6" %} package: name: nanoplot @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanoplot/NanoPlot-{{ version }}.tar.gz - sha256: 1b4988f5ecff5fb732a7d75855b15eaf914d3d2a5f076994eb0fbd2261891449 + sha256: 94157f2d96c4849f5753fc7cc1a7c51e7cc74c20016e46bdd2f7b36d519291b7 build: entry_points: From 1e49cbbb37f4ed6311e4311b5717a9c112db034d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 08:32:13 -0600 Subject: [PATCH 43/80] Update nanoget to 1.19.1 (#41794) * Update nanoget to 1.19.0 * Update nanoget to 1.19.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/nanoget/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nanoget/meta.yaml b/recipes/nanoget/meta.yaml index 7ab273ca7f6430..7b4bab0dbb88de 100644 --- a/recipes/nanoget/meta.yaml +++ b/recipes/nanoget/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.18.1" %} +{% set version = "1.19.1" %} package: name: nanoget @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanoget/nanoget-{{ version }}.tar.gz - sha256: e4fa37ab1bccc3287947f5792acad3c96fd1c02cb9c0a1f5d218d26bcdbe1632 + sha256: 14f4883a995503dbae757b55cb42fcb4430c58ce2201b79abd4e8e0e3d10ca18 build: number: 0 @@ -22,7 +22,6 @@ requirements: - numpy - biopython - pysam >0.10.0 - - nanomath test: imports: @@ -33,3 +32,4 @@ about: license: GPL-3.0-only summary: 'Functions to extract information from Oxford Nanopore sequencing data and alignments.' license_family: GPL + license_file: LICENSE From 727777df1671c18a1914fd9c0615c13dd28b205e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 09:41:36 -0600 Subject: [PATCH 44/80] Update nanocomp to 1.23.1 (#41793) * Update nanocomp to 1.23.0 * Update nanocomp to 1.23.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/nanocomp/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/nanocomp/meta.yaml b/recipes/nanocomp/meta.yaml index 07c2a7629bec97..ed558727d7a4dc 100644 --- a/recipes/nanocomp/meta.yaml +++ b/recipes/nanocomp/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.22.0" %} +{% set version = "1.23.1" %} package: name: nanocomp @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/n/nanocomp/NanoComp-{{ version }}.tar.gz - sha256: e57eb14cc440f2f6809a948caa04e18481c9739c6746d55e6965a55368d9ea7c + sha256: 9c411413e2dec8416f162cbc63996c5a293c1e19c700c67c7137d2103f7f1ded build: entry_points: @@ -24,9 +24,9 @@ requirements: - numpy >=1.16.5 - pandas - pyarrow - - nanoget >=1.4.0 + - nanoget >=1.19.0 - nanomath >=1.0.0 - - NanoPlot >=1.39.0 + - nanoplot >=1.39.0 - psutil - plotly >=3.4.2 From 1b04eccbb12a73723870a810445d12d36d1f6623 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 12:11:31 -0600 Subject: [PATCH 45/80] Update zol to 1.3.2 (#41797) --- recipes/zol/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index fc1cea4af074ab..08b6d2b83410c3 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.3.1" %} +{% set version = "1.3.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: 4de71529288737149441f89c69c33754252a08396e061a2616e15dbfb10121cd + sha256: a97b6ccd94909a11aacc4b6d2474dc02dabcf93da0693f239138c5c52f781518 build: number: 0 From 942fcc8092bbd3c3f1c05d106fa435afbd6d5d83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 13:00:38 -0600 Subject: [PATCH 46/80] Update fastqe to 0.3.1 (#41709) * Update fastqe to 0.3.0 * Update fastqe to 0.3.1 * Update patch --------- Co-authored-by: Brandon Seah --- recipes/fastqe/meta.yaml | 4 ++-- recipes/fastqe/patch | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/fastqe/meta.yaml b/recipes/fastqe/meta.yaml index 917fdaf8b6813f..37ee551c6f5e42 100644 --- a/recipes/fastqe/meta.yaml +++ b/recipes/fastqe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "fastqe" %} -{% set version = "0.2.7" %} +{% set version = "0.3.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: "295788b824ba2fd995cad49aef2e78b1f5b0931a380c3da8530a49e29248b7f4" + sha256: "5b2e60d3d48d9abc5807ebaa9b51c5326b2130b118e0852cd40a35179460379c" patches: - patch diff --git a/recipes/fastqe/patch b/recipes/fastqe/patch index b4226ae43b6620..1a2d2d9debd394 100644 --- a/recipes/fastqe/patch +++ b/recipes/fastqe/patch @@ -1,12 +1,12 @@ diff --git a/setup.py b/setup.py -index 9a34dc5..7fd0d0e 100644 +index a2f0756..12065d8 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,6 @@ setup( license = 'BSD-3-Clause', entry_points = {'console_scripts': ['fastqe = fastqe.fastqe:main']}, install_requires = ["biopython>=1.66",'pyemojify'], -- setup_requires = ['twine>=1.11.0', 'setuptools>=38.6.'], +- setup_requires = ['twine>=1.11.0', 'setuptools>=38.6'], packages = find_packages(exclude=('test', 'docs')), classifiers = [ 'Development Status :: 4 - Beta', From 3eb94697d7558d68b8f38d9c4367926637d3ef4d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sat, 1 Jul 2023 13:01:07 -0600 Subject: [PATCH 47/80] Update pybiolib to 1.1.1065 (#41798) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index e2a7df79b61ad1..329abb595ef222 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1044" %} +{% set version = "1.1.1065" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 92dc8d97bf09d122d779438f9b9d026accf5770b75d40dadbe22b77d015ec561 + sha256: 62c926afcd0a0ad7b48fd9d9a64d9449779458375a9cdebb20c26a46dfcbee8d build: noarch: python From 36fbcbb27f8a47eab66713b4a371077806c431e4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 2 Jul 2023 05:06:10 -0600 Subject: [PATCH 48/80] Update bustools to 0.43.0 (#41799) --- recipes/bustools/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml index 8f909fbda6e2ca..9842c2c986e531 100644 --- a/recipes/bustools/meta.yaml +++ b/recipes/bustools/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.42.0" %} +{% set version = "0.43.0" %} package: name: bustools @@ -6,10 +6,10 @@ package: source: url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz - sha256: 34027724b9c57bdbf2e7c252962e30c329b3f5f9fc03d10a5feef336ce50d008 + sha256: a881fd273e4242a422a60e69b2d47210880fba855346a13efbc5480e7a2f9721 build: - number: 2 + number: 0 requirements: build: From b1857848d478810dd9a6fc501d9b4c2c9cf4a537 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 2 Jul 2023 05:40:54 -0600 Subject: [PATCH 49/80] Update perbase to 0.9.0 (#41599) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Christian Brueffer Co-authored-by: Björn Grüning --- recipes/perbase/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perbase/meta.yaml b/recipes/perbase/meta.yaml index a5926cd99560d8..dde88d675f88fc 100644 --- a/recipes/perbase/meta.yaml +++ b/recipes/perbase/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.5" %} -{% set sha256 = "15a3ec701ab771abe017b8ea1df9a1668070e6817996ea12ae9750f57e99f54a" %} +{% set version = "0.9.0" %} +{% set sha256 = "8f3c4ef2475241e06636c9e2790da5258aac69722d6fbc8592b33a6bfeb49ddb" %} package: name: perbase @@ -10,7 +10,7 @@ source: sha256: {{ sha256 }} build: - number: 3 + number: 0 requirements: build: From fdbaa9159a2dd9b3772caac917d43af2fcfeb48b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 2 Jul 2023 08:13:29 -0600 Subject: [PATCH 50/80] Update perl-statistics-descriptive to 3.0801 (#41800) --- recipes/perl-statistics-descriptive/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/perl-statistics-descriptive/meta.yaml b/recipes/perl-statistics-descriptive/meta.yaml index 146ae518e3cbe0..e1332d2f63e5e9 100644 --- a/recipes/perl-statistics-descriptive/meta.yaml +++ b/recipes/perl-statistics-descriptive/meta.yaml @@ -1,10 +1,10 @@ package: name: perl-statistics-descriptive - version: "3.0800" + version: "3.0801" source: - url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0800.tar.gz - sha256: b04edeea26bfed435aa6029956798c281f7f52d4545f3f45b2ad44954e96f939 + url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0801.tar.gz + sha256: 047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65 build: noarch: generic From f9bd84d28bce761fa3faf8a8361cecb3b67abbf6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 2 Jul 2023 11:45:53 -0600 Subject: [PATCH 51/80] Update taxpasta to 0.4.0 (#41802) --- recipes/taxpasta/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/taxpasta/meta.yaml b/recipes/taxpasta/meta.yaml index a5c8b1d6af60fb..0595ea3dae406a 100644 --- a/recipes/taxpasta/meta.yaml +++ b/recipes/taxpasta/meta.yaml @@ -1,6 +1,6 @@ {% set name = "taxpasta" %} -{% set version = "0.3.0" %} -{% set sha256 = "f6abbed1c9100a0dbb8546ee88452ac0ddace5870eb6e211f100f4644a79f749" %} +{% set version = "0.4.0" %} +{% set sha256 = "8a0c95478845c2a2c041083620c17b99dd3b085b8677f7dae3341b5bd6d8f2bf" %} package: name: {{ name|lower }} From 776a29841080812f6cbaa7afd317376fb1aa17f7 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Sun, 2 Jul 2023 14:35:20 -0600 Subject: [PATCH 52/80] Update rustybam to 0.1.33 (#41805) * Update rustybam to 0.1.33 * Update meta.yaml --------- Co-authored-by: Mitchell Robert Vollger --- recipes/rustybam/meta.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/rustybam/meta.yaml b/recipes/rustybam/meta.yaml index 30d584b5e079c9..50a07db88c9045 100644 --- a/recipes/rustybam/meta.yaml +++ b/recipes/rustybam/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "0.1.31" %} +{% set version = "0.1.33" %} package: name: rustybam version: {{ version }} build: - number: 2 + number: 0 source: url: https://github.com/mrvollger/rustybam/archive/v{{ version }}.tar.gz - sha256: 6c1a66f759d6583be6ec3e6962e3d7f69a923dedee4e6a8d7595c00496127bf3 + sha256: d1f449063fc6974d8dfa94566c91de7b15ce9cf84e0665d65e5e80e0815b8f1b requirements: build: @@ -46,3 +46,8 @@ about: home: https://github.com/mrvollger/rustybam license: MIT summary: Mitchell Vollger's bioinformatics rust utilities. + +extra: + recipe-maintainers: + - mrvollger + From 19c11afef645f461dfd3d75b6a79f10b29e894b1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 03:45:31 -0600 Subject: [PATCH 53/80] Update r-dartr to 2.9.7 (#41373) * Update r-dartr to 2.9.7 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/r-dartr/meta.yaml | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/recipes/r-dartr/meta.yaml b/recipes/r-dartr/meta.yaml index 833f7791db2238..f07414b3f6c51a 100644 --- a/recipes/r-dartr/meta.yaml +++ b/recipes/r-dartr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '2.0.4' %} +{% set version = '2.9.7' %} package: name: r-dartr @@ -8,10 +8,10 @@ source: url: - {{ cran_mirror }}/src/contrib/dartR_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/dartR/dartR_{{ version }}.tar.gz - sha256: 45ba82bfc5fb193d128a02a48b48855d16378133e0a85bb8870406466a8cd8a2 + sha256: 7d8f7467f6d7c5514531bb0fb7917ae0e28eedec4fc3a0b404890e72f01395f3 build: - number: 1 + number: 0 noarch: generic rpaths: - lib/R/lib/ @@ -20,7 +20,6 @@ build: requirements: host: - r-base - - r-hardyweinberg - r-mass - r-popgenreport - bioconductor-snprelate @@ -28,24 +27,24 @@ requirements: - r-adegenet >=2.0.0 - r-ape - r-crayon - - r-devtools + - r-dartr.data + - r-data.table - r-dplyr + - r-fields - r-foreach - r-ggplot2 - r-gridextra - - r-hierfstat + - r-patchwork - r-plyr - r-raster - r-reshape2 - - r-sp + - r-shiny + - r-sp >=1.6.1 - r-stringr - r-tidyr - r-vegan - - r-fields - - r-patchwork run: - r-base - - r-hardyweinberg - r-mass - r-popgenreport - bioconductor-snprelate @@ -53,21 +52,22 @@ requirements: - r-adegenet >=2.0.0 - r-ape - r-crayon - - r-devtools + - r-dartr.data + - r-data.table - r-dplyr + - r-fields - r-foreach - r-ggplot2 - r-gridextra - - r-hierfstat + - r-patchwork - r-plyr - r-raster - r-reshape2 - - r-sp + - r-shiny + - r-sp >=1.6.1 - r-stringr - r-tidyr - r-vegan - - r-fields - - r-patchwork test: commands: @@ -75,7 +75,7 @@ test: about: home: https://CRAN.R-project.org/package=dartR - license: GPL-2.0-only + license: GPL-3.0-or-later summary: Functions are provided that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment @@ -87,6 +87,6 @@ about: are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages. - license_family: GPL2 + license_family: GPL3 license_file: - - {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2 + - {{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3 From db6959a09d295e6ee737ecc9a82ee554cb696e6d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 04:16:30 -0600 Subject: [PATCH 54/80] Update checkqc to 3.8.1 (#41806) * Update checkqc to 3.8.1 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/checkqc/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml index 0a5124a15c6232..437ec826db435f 100644 --- a/recipes/checkqc/meta.yaml +++ b/recipes/checkqc/meta.yaml @@ -1,5 +1,5 @@ {% set name = "checkQC" %} -{% set version = "3.8.0" %} +{% set version = "3.8.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c40378e47060d187c628677bd30c4c66ae9c0e9d91ac250b865ed175d287772f + sha256: 05581afe99b37d3c1ee5a383b92fd9381e7a20caa54fe43f7e9f6b5a325a9058 build: number: 0 @@ -23,10 +23,10 @@ requirements: - python >=3.6 run: - click - - illumina-interop >=1.1.10 + - illumina-interop >=1.2.3 - python >=3.6 - pyyaml >=3.12 - - sample-sheet + - sample-sheet >=0.13.0 - tornado - xmltodict From 78451990e4607d4de371b459f12f3ebca11ba921 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 05:53:55 -0600 Subject: [PATCH 55/80] Update pcaone to 0.3.4 (#41804) --- recipes/pcaone/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml index 64c6da8c047463..0ad03afefb34d7 100644 --- a/recipes/pcaone/meta.yaml +++ b/recipes/pcaone/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.3" %} -{% set sha256 = "dd00840d35c6e156c979110cf978f53a8e72ebe3dfb649d4c22d462dfb070a9f" %} +{% set version = "0.3.4" %} +{% set sha256 = "6d767af1f7a7df8741c2440d155e45c3536981aa9d13f7cd229ef7318a81b349" %} package: From 6bf84f7a8269b5f919d07a2b6ebd20306bf82620 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 06:36:03 -0600 Subject: [PATCH 56/80] Update genome_updater to 0.6.3 (#41807) --- recipes/genome_updater/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genome_updater/meta.yaml b/recipes/genome_updater/meta.yaml index 360da62cc2da66..73918265bbcfd7 100755 --- a/recipes/genome_updater/meta.yaml +++ b/recipes/genome_updater/meta.yaml @@ -1,5 +1,5 @@ {% set name = "genome_updater" %} -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/pirovc/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 9531bbd35df5290927dd320acb151ca6212108e78ffe5a9eb0dd463585ebdce7 + sha256: 07171e3d7f6973e98599b2b594f41655a8249478f94f56c4f09f2fc13ec70060 build: From c58062fea54e3aa4459bef44de20cb642661b298 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Mon, 3 Jul 2023 15:02:31 +0200 Subject: [PATCH 57/80] [pmx_biobb] update 4.1.2 (#41808) --- recipes/pmx_biobb/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index 0a0605ee0765da..8746c50713770c 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -1,8 +1,8 @@ {% set name = "pmx_biobb" %} -{% set version = "4.0.2" %} +{% set version = "4.1.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "3c3faafe44109f95f0d804e677da0240f8a936d866cc773c0a53dccbc00b5b21" %} +{% set hash_value = "11a2ec951c376f51990c9b2c08f4112122a1e538076e9fe6e90cc0dbd4e5e856" %} package: name: '{{ name|lower }}' @@ -24,13 +24,13 @@ requirements: - {{ compiler('fortran') }} - make host: - - python + - python >=3.7 - setuptools - scipy - matplotlib-base - rdkit run: - - python + - python >=3.7 - scipy - matplotlib-base - rdkit From 66f6b06f173578177d83458473e6f38d62ffb69e Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Mon, 3 Jul 2023 16:35:10 +0200 Subject: [PATCH 58/80] [pmx_biobb] update 4.1.2 build 1: Python 3.7 (#41809) * [pmx_biobb] update 4.1.2 build 1: Python 3.7 * Update meta.yaml * Update meta.yaml --- recipes/pmx_biobb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index 8746c50713770c..ae99187bd9df65 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 0 + number: 1 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,13 +24,13 @@ requirements: - {{ compiler('fortran') }} - make host: - - python >=3.7 + - python =3.7 - setuptools - scipy - matplotlib-base - rdkit run: - - python >=3.7 + - python =3.7 - scipy - matplotlib-base - rdkit From b6771bc135571babf14e4285e4663b29ca47ca84 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 3 Jul 2023 15:18:50 -0600 Subject: [PATCH 59/80] Update r-cellosaurus to 0.5.4 (#41817) --- recipes/r-cellosaurus/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-cellosaurus/meta.yaml b/recipes/r-cellosaurus/meta.yaml index ab8fc879721c52..a04d61cd0b7a78 100644 --- a/recipes/r-cellosaurus/meta.yaml +++ b/recipes/r-cellosaurus/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} {% set github = "https://github.com/acidgenomics/r-cellosaurus" %} package: @@ -7,7 +7,7 @@ package: source: url: "{{ github }}/archive/v{{ version }}.tar.gz" - sha256: 1b46d192c9abf1c0668d30625b8fefa0046a8a5ff1baa3ba01fe90f11fb5f562 + sha256: 51a2895971a70e6d4eddf1db40e0d1641ac7a9c88036b8c34171014241e1fda2 build: noarch: generic From 82325d9207a7c290a09ab498c3feba2a433cb9c4 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 4 Jul 2023 06:46:05 +0200 Subject: [PATCH 60/80] [pmx_biobb] update 4.1.2 build 2: Python [no vers] (#41812) --- recipes/pmx_biobb/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pmx_biobb/meta.yaml b/recipes/pmx_biobb/meta.yaml index ae99187bd9df65..c711e8d8d62ec0 100644 --- a/recipes/pmx_biobb/meta.yaml +++ b/recipes/pmx_biobb/meta.yaml @@ -13,7 +13,7 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" @@ -24,13 +24,13 @@ requirements: - {{ compiler('fortran') }} - make host: - - python =3.7 + - python - setuptools - scipy - matplotlib-base - rdkit run: - - python =3.7 + - python - scipy - matplotlib-base - rdkit From defb45d4dc7e6154460af5bd56001397763551ec Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Tue, 4 Jul 2023 09:23:42 +0200 Subject: [PATCH 61/80] Update MoDLE to v1.1.0 (#41060) * Bump version * Add integration tests * test.sh -> run_test.sh * Bugfix * Bugfix * Bugfix * Debugging * Debugging * Bugfix * Try to manually specify conan profiles * Simplify a bit * Fix typos * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Bugfix * Let's try to simplify things... * Linux CI is working fine: let's skip it for now * Try to see if this compilation error only affects boost * The problem seems to be only with boost. Let's focus on that * Try to build boost and its deps in two stages * Bugfix * debugging compilation issues on macOS is fun... * Bugfix * Try to bump boost * Build b2 * Debugging * Debugging * Debugging * Update url * Update url * Lucky me, a compiler segfault... * Debug test failure * Remove unnecessary files * Fix sed on MacOS * Install shasum* * Update URL --------- Co-authored-by: Devon Ryan --- recipes/modle/build.sh | 19 ++-- recipes/modle/build_failure.linux-64.yaml | 104 ---------------------- recipes/modle/build_failure.osx-64.yaml | 104 ---------------------- recipes/modle/conan_profiles/clang | 9 ++ recipes/modle/conan_profiles/gcc | 8 ++ recipes/modle/cross-linux.cmake | 1 + recipes/modle/meta.yaml | 21 ++++- recipes/modle/run_test.sh | 24 +++++ 8 files changed, 71 insertions(+), 219 deletions(-) delete mode 100644 recipes/modle/build_failure.linux-64.yaml delete mode 100644 recipes/modle/build_failure.osx-64.yaml create mode 100644 recipes/modle/conan_profiles/clang create mode 100644 recipes/modle/conan_profiles/gcc create mode 100755 recipes/modle/run_test.sh diff --git a/recipes/modle/build.sh b/recipes/modle/build.sh index 48989353034b5d..af31fd2fb2785c 100755 --- a/recipes/modle/build.sh +++ b/recipes/modle/build.sh @@ -17,15 +17,17 @@ export CONAN_HOME="$scratch/conan" # shellcheck disable=SC2064 trap "rm -rf '$scratch'" EXIT +# Conan doesn't detect compiler name and version when using cc/c++ +TMPBIN="$scratch/bin" +mkdir "$TMPBIN" + declare -a CMAKE_PLATFORM_FLAGS if [[ ${HOST} =~ .*darwin.* ]]; then export MACOSX_DEPLOYMENT_TARGET=10.15 # Required to use std::filesystem CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}") + conan_profile='clang' else CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake") - # Conan doesn't detect compiler name and version when using cc/c++ - TMPBIN="$scratch/bin" - mkdir "$TMPBIN" ln -sf "$CC" "$TMPBIN/gcc" ln -sf "$CXX" "$TMPBIN/g++" @@ -33,15 +35,18 @@ else export PATH="$TMPBIN:$PATH" export CC="$TMPBIN/gcc" export CXX="$TMPBIN/g++" + conan_profile='gcc' fi -conan profile detect +# Remember to update these profiles when bioconda's compiler toolchains are updated +mkdir -p "$CONAN_HOME/profiles/" +ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/$conan_profile" -# Build everything from source to avoid ABI issues due to old GLIBC/GLIBCXX conan install conanfile.txt \ --build="*" \ - -s build_type=Release \ - -s compiler.cppstd=17 \ + --build="b2/*" \ + -pr:b "$conan_profile" \ + -pr:h "$conan_profile" \ --output-folder=build/ # Add bioconda suffix to MoDLE version diff --git a/recipes/modle/build_failure.linux-64.yaml b/recipes/modle/build_failure.linux-64.yaml deleted file mode 100644 index aea7250a1291e6..00000000000000 --- a/recipes/modle/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 251bacb41264d22c9c003d1390440d9f4ca356b10623ac2fbc0802978e083d6d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - bshoshany-thread-pool/3.3.0:[0m Checking remote: conancenter[0m - bshoshany-thread-pool/3.3.0:[0m Downloaded recipe revision 22e99aee6babc19e679754d95dad2de4[0m - catch2/3.3.2:[0m Not found in local cache, looking in remotes...[0m - catch2/3.3.2:[0m Checking remote: conancenter[0m - catch2/3.3.2:[0m Downloaded recipe revision be6a2f0225146ba4fd8573ee9013e5ae[0m - cli11/2.3.2:[0m Not found in local cache, looking in remotes...[0m - cli11/2.3.2:[0m Checking remote: conancenter[0m - cli11/2.3.2:[0m Downloaded recipe revision 8ccdf14fb1ad53532d498c16ae580b4b[0m - concurrentqueue/1.0.3:[0m Not found in local cache, looking in remotes...[0m - concurrentqueue/1.0.3:[0m Checking remote: conancenter[0m - concurrentqueue/1.0.3:[0m Downloaded recipe revision c1cb7d960d8b64073643b45fa63f0bd1[0m - cpp-sort/1.14.0:[0m Not found in local cache, looking in remotes...[0m - cpp-sort/1.14.0:[0m Checking remote: conancenter[0m - cpp-sort/1.14.0:[0m Downloaded recipe revision 3453aaaf83c1dae4214ca3b5c4c3a5c8[0m - fast_float/4.0.0:[0m Not found in local cache, looking in remotes...[0m - fast_float/4.0.0:[0m Checking remote: conancenter[0m - fast_float/4.0.0:[0m Downloaded recipe revision 90cac63d3ae321f6318b9abf8af9cbb1[0m - fmt/9.1.0:[0m Not found in local cache, looking in remotes...[0m - fmt/9.1.0:[0m Checking remote: conancenter[0m - fmt/9.1.0:[0m Downloaded recipe revision e747928f85b03f48aaf227ff897d9634[0m - hdf5/1.14.0:[0m Not found in local cache, looking in remotes...[0m - hdf5/1.14.0:[0m Checking remote: conancenter[0m - hdf5/1.14.0:[0m Downloaded recipe revision 011206975dc4c5ca80dd612d3a34cab3[0m - cmake/3.26.4:[0m Not found in local cache, looking in remotes...[0m - cmake/3.26.4:[0m Checking remote: conancenter[0m - cmake/3.26.4:[0m Downloaded recipe revision 0b40747e190e755932767f2ec4768ff5[0m - highfive/2.7.1:[0m Not found in local cache, looking in remotes...[0m - highfive/2.7.1:[0m Checking remote: conancenter[0m - highfive/2.7.1:[0m Downloaded recipe revision a73bc6937c9add30c9d47a7a70a466eb[0m - libarchive/3.6.2:[0m Not found in local cache, looking in remotes...[0m - libarchive/3.6.2:[0m Checking remote: conancenter[0m - libarchive/3.6.2:[0m Downloaded recipe revision b768ab8c0dcfb9e27b912a7f32fd02c1[0m - libiconv/1.17:[0m Not found in local cache, looking in remotes...[0m - libiconv/1.17:[0m Checking remote: conancenter[0m - libiconv/1.17:[0m Downloaded recipe revision fa54397801cd96911a8294bc5fc76335[0m - lz4/1.9.4:[0m Not found in local cache, looking in remotes...[0m - lz4/1.9.4:[0m Checking remote: conancenter[0m - lz4/1.9.4:[0m Downloaded recipe revision bce1f314775b83c195dffc8e177ff368[0m - lzo/2.10:[0m Not found in local cache, looking in remotes...[0m - lzo/2.10:[0m Checking remote: conancenter[0m - lzo/2.10:[0m Downloaded recipe revision 5725914235423c771cb1c6b607109b45[0m - libbigwig/0.4.7:[0m Not found in local cache, looking in remotes...[0m - libbigwig/0.4.7:[0m Checking remote: conancenter[0m - libbigwig/0.4.7:[0m Downloaded recipe revision 97113380bd925b2220b1d1e63c454d91[0m - zlib-ng/2.0.7:[0m Not found in local cache, looking in remotes...[0m - zlib-ng/2.0.7:[0m Checking remote: conancenter[0m - zlib-ng/2.0.7:[0m Downloaded recipe revision fbf3d453595da4be4245283c4ca065b8[0m - libcuckoo/0.3.1:[0m Not found in local cache, looking in remotes...[0m - libcuckoo/0.3.1:[0m Checking remote: conancenter[0m - libcuckoo/0.3.1:[0m Downloaded recipe revision 7e514d4c23a9aba3d8d80758824e9dc0[0m - [1m[33mGraph root[0m - [1m[36m conanfile.txt: /opt/conda/conda-bld/modle_1686044039950/work/conanfile.txt[0m - [1m[33mRequirements[0m - [1m[36m abseil/20230125.3#5431a4c609f5fb48bb8d8567e953243f - Downloaded (conancenter)[0m - [1m[36m bitflags/1.5.0#626da9d1913161321841f30caf9b994e - Downloaded (conancenter)[0m - [1m[36m boost/1.81.0#9bd7ae86a881631b6cc76590621e470b - Downloaded (conancenter)[0m - [1m[36m bshoshany-thread-pool/3.3.0#22e99aee6babc19e679754d95dad2de4 - Downloaded (conancenter)[0m - [1m[36m bzip2/1.0.8#411fc05e80d47a89045edc1ee6f23c1d - Downloaded (conancenter)[0m - [1m[36m catch2/3.3.2#be6a2f0225146ba4fd8573ee9013e5ae - Downloaded (conancenter)[0m - [1m[36m cli11/2.3.2#8ccdf14fb1ad53532d498c16ae580b4b - Downloaded (conancenter)[0m - [1m[36m concurrentqueue/1.0.3#c1cb7d960d8b64073643b45fa63f0bd1 - Downloaded (conancenter)[0m - [1m[36m cpp-sort/1.14.0#3453aaaf83c1dae4214ca3b5c4c3a5c8 - Downloaded (conancenter)[0m - [1m[36m fast_float/4.0.0#90cac63d3ae321f6318b9abf8af9cbb1 - Downloaded (conancenter)[0m - [1m[36m fmt/9.1.0#e747928f85b03f48aaf227ff897d9634 - Downloaded (conancenter)[0m - [1m[36m hdf5/1.14.0#011206975dc4c5ca80dd612d3a34cab3 - Downloaded (conancenter)[0m - [1m[36m highfive/2.7.1#a73bc6937c9add30c9d47a7a70a466eb - Downloaded (conancenter)[0m - [1m[36m libarchive/3.6.2#b768ab8c0dcfb9e27b912a7f32fd02c1 - Downloaded (conancenter)[0m - [1m[36m libbigwig/0.4.7#97113380bd925b2220b1d1e63c454d91 - Downloaded (conancenter)[0m - [1m[36m libcuckoo/0.3.1#7e514d4c23a9aba3d8d80758824e9dc0 - Downloaded (conancenter)[0m - [1m[36m libiconv/1.17#fa54397801cd96911a8294bc5fc76335 - Downloaded (conancenter)[0m - [1m[36m lz4/1.9.4#bce1f314775b83c195dffc8e177ff368 - Downloaded (conancenter)[0m - [1m[36m lzo/2.10#5725914235423c771cb1c6b607109b45 - Downloaded (conancenter)[0m - [1m[36m xz_utils/5.4.2#b6ee8320403def553418874435445982 - Downloaded (conancenter)[0m - [1m[36m zlib/1.2.13#e377bee636333ae348d51ca90874e353 - Downloaded (conancenter)[0m - [1m[36m zlib-ng/2.0.7#fbf3d453595da4be4245283c4ca065b8 - Downloaded (conancenter)[0m - [1m[36m zstd/1.5.5#93372fe14bb7883bd4de82914e0a1841 - Downloaded (conancenter)[0m - [1m[33mBuild requirements[0m - [1m[36m b2/4.9.6#2e02945ad41739b8051247d14fe8297d - Downloaded (conancenter)[0m - [1m[36m cmake/3.26.4#0b40747e190e755932767f2ec4768ff5 - Downloaded (conancenter)[0m - [1m[33mResolved version ranges[0m - [1m[36m cmake/[>=3.18 <4]: cmake/3.26.4[0m - [31mERROR: Version conflict: None->lzo/2.10, None->lzo/2.10.[0m - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/modle_1686044039950/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/modle/build_failure.osx-64.yaml b/recipes/modle/build_failure.osx-64.yaml deleted file mode 100644 index d2c99f037b8fe9..00000000000000 --- a/recipes/modle/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 251bacb41264d22c9c003d1390440d9f4ca356b10623ac2fbc0802978e083d6d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - bshoshany-thread-pool/3.3.0: Checking remote: conancenter - bshoshany-thread-pool/3.3.0: Downloaded recipe revision 22e99aee6babc19e679754d95dad2de4 - catch2/3.3.2: Not found in local cache, looking in remotes... - catch2/3.3.2: Checking remote: conancenter - catch2/3.3.2: Downloaded recipe revision be6a2f0225146ba4fd8573ee9013e5ae - cli11/2.3.2: Not found in local cache, looking in remotes... - cli11/2.3.2: Checking remote: conancenter - cli11/2.3.2: Downloaded recipe revision 8ccdf14fb1ad53532d498c16ae580b4b - concurrentqueue/1.0.3: Not found in local cache, looking in remotes... - concurrentqueue/1.0.3: Checking remote: conancenter - concurrentqueue/1.0.3: Downloaded recipe revision c1cb7d960d8b64073643b45fa63f0bd1 - cpp-sort/1.14.0: Not found in local cache, looking in remotes... - cpp-sort/1.14.0: Checking remote: conancenter - cpp-sort/1.14.0: Downloaded recipe revision 3453aaaf83c1dae4214ca3b5c4c3a5c8 - fast_float/4.0.0: Not found in local cache, looking in remotes... - fast_float/4.0.0: Checking remote: conancenter - fast_float/4.0.0: Downloaded recipe revision 90cac63d3ae321f6318b9abf8af9cbb1 - fmt/9.1.0: Not found in local cache, looking in remotes... - fmt/9.1.0: Checking remote: conancenter - fmt/9.1.0: Downloaded recipe revision e747928f85b03f48aaf227ff897d9634 - hdf5/1.14.0: Not found in local cache, looking in remotes... - hdf5/1.14.0: Checking remote: conancenter - hdf5/1.14.0: Downloaded recipe revision 011206975dc4c5ca80dd612d3a34cab3 - cmake/3.26.4: Not found in local cache, looking in remotes... - cmake/3.26.4: Checking remote: conancenter - cmake/3.26.4: Downloaded recipe revision 0b40747e190e755932767f2ec4768ff5 - highfive/2.7.1: Not found in local cache, looking in remotes... - highfive/2.7.1: Checking remote: conancenter - highfive/2.7.1: Downloaded recipe revision a73bc6937c9add30c9d47a7a70a466eb - libarchive/3.6.2: Not found in local cache, looking in remotes... - libarchive/3.6.2: Checking remote: conancenter - libarchive/3.6.2: Downloaded recipe revision b768ab8c0dcfb9e27b912a7f32fd02c1 - libiconv/1.17: Not found in local cache, looking in remotes... - libiconv/1.17: Checking remote: conancenter - libiconv/1.17: Downloaded recipe revision fa54397801cd96911a8294bc5fc76335 - lz4/1.9.4: Not found in local cache, looking in remotes... - lz4/1.9.4: Checking remote: conancenter - lz4/1.9.4: Downloaded recipe revision bce1f314775b83c195dffc8e177ff368 - lzo/2.10: Not found in local cache, looking in remotes... - lzo/2.10: Checking remote: conancenter - lzo/2.10: Downloaded recipe revision 5725914235423c771cb1c6b607109b45 - libbigwig/0.4.7: Not found in local cache, looking in remotes... - libbigwig/0.4.7: Checking remote: conancenter - libbigwig/0.4.7: Downloaded recipe revision 97113380bd925b2220b1d1e63c454d91 - zlib-ng/2.0.7: Not found in local cache, looking in remotes... - zlib-ng/2.0.7: Checking remote: conancenter - zlib-ng/2.0.7: Downloaded recipe revision fbf3d453595da4be4245283c4ca065b8 - libcuckoo/0.3.1: Not found in local cache, looking in remotes... - libcuckoo/0.3.1: Checking remote: conancenter - libcuckoo/0.3.1: Downloaded recipe revision 7e514d4c23a9aba3d8d80758824e9dc0 - Graph root - conanfile.txt: /opt/mambaforge/envs/bioconda/conda-bld/modle_1686044682356/work/conanfile.txt - Requirements - abseil/20230125.3#5431a4c609f5fb48bb8d8567e953243f - Downloaded (conancenter) - bitflags/1.5.0#626da9d1913161321841f30caf9b994e - Downloaded (conancenter) - boost/1.81.0#9bd7ae86a881631b6cc76590621e470b - Downloaded (conancenter) - bshoshany-thread-pool/3.3.0#22e99aee6babc19e679754d95dad2de4 - Downloaded (conancenter) - bzip2/1.0.8#411fc05e80d47a89045edc1ee6f23c1d - Downloaded (conancenter) - catch2/3.3.2#be6a2f0225146ba4fd8573ee9013e5ae - Downloaded (conancenter) - cli11/2.3.2#8ccdf14fb1ad53532d498c16ae580b4b - Downloaded (conancenter) - concurrentqueue/1.0.3#c1cb7d960d8b64073643b45fa63f0bd1 - Downloaded (conancenter) - cpp-sort/1.14.0#3453aaaf83c1dae4214ca3b5c4c3a5c8 - Downloaded (conancenter) - fast_float/4.0.0#90cac63d3ae321f6318b9abf8af9cbb1 - Downloaded (conancenter) - fmt/9.1.0#e747928f85b03f48aaf227ff897d9634 - Downloaded (conancenter) - hdf5/1.14.0#011206975dc4c5ca80dd612d3a34cab3 - Downloaded (conancenter) - highfive/2.7.1#a73bc6937c9add30c9d47a7a70a466eb - Downloaded (conancenter) - libarchive/3.6.2#b768ab8c0dcfb9e27b912a7f32fd02c1 - Downloaded (conancenter) - libbigwig/0.4.7#97113380bd925b2220b1d1e63c454d91 - Downloaded (conancenter) - libcuckoo/0.3.1#7e514d4c23a9aba3d8d80758824e9dc0 - Downloaded (conancenter) - libiconv/1.17#fa54397801cd96911a8294bc5fc76335 - Downloaded (conancenter) - lz4/1.9.4#bce1f314775b83c195dffc8e177ff368 - Downloaded (conancenter) - lzo/2.10#5725914235423c771cb1c6b607109b45 - Downloaded (conancenter) - xz_utils/5.4.2#b6ee8320403def553418874435445982 - Downloaded (conancenter) - zlib/1.2.13#e377bee636333ae348d51ca90874e353 - Downloaded (conancenter) - zlib-ng/2.0.7#fbf3d453595da4be4245283c4ca065b8 - Downloaded (conancenter) - zstd/1.5.5#93372fe14bb7883bd4de82914e0a1841 - Downloaded (conancenter) - Build requirements - b2/4.9.6#2e02945ad41739b8051247d14fe8297d - Downloaded (conancenter) - cmake/3.26.4#0b40747e190e755932767f2ec4768ff5 - Downloaded (conancenter) - Resolved version ranges - cmake/[>=3.18 <4]: cmake/3.26.4 - ERROR: Version conflict: None->lzo/2.10, None->lzo/2.10. - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/modle_1686044682356/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/modle/conan_profiles/clang b/recipes/modle/conan_profiles/clang new file mode 100644 index 00000000000000..efb06428a92bc5 --- /dev/null +++ b/recipes/modle/conan_profiles/clang @@ -0,0 +1,9 @@ +[settings] +arch=x86_64 +build_type=Release +compiler=clang +compiler.cppstd=17 +compiler.libcxx=libc++ +compiler.version=14 +os=Macos +os.version="10.15" diff --git a/recipes/modle/conan_profiles/gcc b/recipes/modle/conan_profiles/gcc new file mode 100644 index 00000000000000..ef7e2f6219ff18 --- /dev/null +++ b/recipes/modle/conan_profiles/gcc @@ -0,0 +1,8 @@ +[settings] +arch=x86_64 +build_type=Release +compiler=gcc +compiler.cppstd=17 +compiler.libcxx=libstdc++11 +compiler.version=13 +os=Linux diff --git a/recipes/modle/cross-linux.cmake b/recipes/modle/cross-linux.cmake index bb837eea5ba7b1..b8f90c3409b9d9 100644 --- a/recipes/modle/cross-linux.cmake +++ b/recipes/modle/cross-linux.cmake @@ -6,6 +6,7 @@ set(CMAKE_SYSTEM_VERSION 1) # specify the cross compiler set(CMAKE_C_COMPILER $ENV{CC}) +set(CMAKE_CXX_COMPILER $ENV{CXX}) # where is the target environment set(CMAKE_FIND_ROOT_PATH $ENV{PREFIX} $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot) diff --git a/recipes/modle/meta.yaml b/recipes/modle/meta.yaml index 40f78ad373145d..602ba4b530f812 100644 --- a/recipes/modle/meta.yaml +++ b/recipes/modle/meta.yaml @@ -1,13 +1,13 @@ {% set name = "MoDLE" %} -{% set version = "1.0.1" %} -{% set sha256 = "66135d77127abac89fae1309346decd179a96ba512ded58dbdc3a8c802ca87f7" %} +{% set version = "1.1.0" %} +{% set sha256 = "f1bfd2c98ff131d555bc1504fab5c86f35521e51da87d5f66435c145e11a26e3" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 source: url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz @@ -17,7 +17,7 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - cmake >=3.20 + - cmake >=3.25 - conan >=2.0 - git >2.7 - make @@ -31,6 +31,19 @@ about: doc_url: https://github.com/paulsengroup/{{ name }}#readme test: + requires: + - cooler>=0.9 + - curl + - perl-digest-sha1 + - pyBigWig>=0.3.22 + - xz + source_files: + - cmake/FetchTestDataset.cmake + - test/scripts/compare_bwigs.py + - test/scripts/modle_integration_test.sh + - test/scripts/modle_tools_annotate_barriers_integration_test.sh + - test/scripts/modle_tools_eval_integration_test.sh + - test/scripts/modle_tools_transform_integration_test.sh commands: - modle --help - modle_tools --help diff --git a/recipes/modle/run_test.sh b/recipes/modle/run_test.sh new file mode 100755 index 00000000000000..9c188aa3242f44 --- /dev/null +++ b/recipes/modle/run_test.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +set -e +set -u +set -x +set -o pipefail + +# Extract test dataset URL and checksum +url="$(grep -F 'DOWNLOAD' 'cmake/FetchTestDataset.cmake' | sed -E 's/.*DOWNLOAD[[:space:]]+//')" +checksum="$(grep -F 'EXPECTED_HASH' 'cmake/FetchTestDataset.cmake' | sed 's/.*SHA512=//')" + +# Download and extract test datasets +curl -L "$url" -o modle_test_dataset.tar.xz +echo "$checksum modle_test_dataset.tar.xz" > checksum.sha512 +shasum -c checksum.sha512 + +tar -xf modle_test_dataset.tar.xz test/data/integration_tests/ + +# Run integration tests +test/scripts/modle_integration_test.sh "$(which modle)" + +test/scripts/modle_tools_annotate_barriers_integration_test.sh "$(which modle_tools)" +test/scripts/modle_tools_eval_integration_test.sh "$(which modle_tools)" +test/scripts/modle_tools_transform_integration_test.sh "$(which modle_tools)" From 0a4ce74098625614dc025d29961adf2886cba318 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 4 Jul 2023 09:59:14 +0200 Subject: [PATCH 62/80] Scirpy: unpin pandas (#41821) v0.13 is compatible with pandas 2.0. Forgot to remove the constraints during autobump. Fixes https://github.com/scverse/scirpy/issues/426 --- recipes/scirpy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scirpy/meta.yaml b/recipes/scirpy/meta.yaml index a925157bea8ff7..0304c3f0005404 100644 --- a/recipes/scirpy/meta.yaml +++ b/recipes/scirpy/meta.yaml @@ -11,7 +11,7 @@ source: folder: "{{ name }}-{{ version }}" build: - number: 0 + number: 1 noarch: python script: - cd "{{ name }}-{{ version }}" @@ -29,7 +29,7 @@ requirements: - awkward >=2.1.0 - mudata >=0.2.3 - scanpy >=1.9.3 - - pandas >=1.5,<2 + - pandas >=1.5 - numpy >=1.17.0 - scipy - parasail-python From dd5adee4ce14be385b5ed726622a6965137f7ec9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 02:31:45 -0600 Subject: [PATCH 63/80] Update treeswift to 1.1.37 (#41814) * Update treeswift to 1.1.36 * Update treeswift to 1.1.37 --- recipes/treeswift/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/treeswift/meta.yaml b/recipes/treeswift/meta.yaml index a7e9f6c83b3486..29ddb697dd74e7 100644 --- a/recipes/treeswift/meta.yaml +++ b/recipes/treeswift/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.35" %} +{% set version = "1.1.37" %} package: name: "treeswift" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/t/treeswift/treeswift-{{ version }}.tar.gz - sha256: cbe615f48681146adc643ead9ca4bbf1b3d65aeedb0aa6d0495086cf316d3668 + sha256: d7899104428cbb157027099fbe2fbaec1e87870ae48d561a6075a29498827b6b build: noarch: python From 0d9160a27e3d08502ed3c0d0e59f19aded4cc8a5 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Tue, 4 Jul 2023 13:20:52 +0200 Subject: [PATCH 64/80] Equivalent to #40459 (#41823) Co-authored-by: Devon Ryan --- recipes/dropest/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/dropest/meta.yaml b/recipes/dropest/meta.yaml index 1b1fe9b12cdab1..281e7c2d09ed4a 100644 --- a/recipes/dropest/meta.yaml +++ b/recipes/dropest/meta.yaml @@ -12,7 +12,7 @@ source: - patch build: - number: 6 + number: 7 skip: True # [osx] rpaths: - lib/R/lib/ @@ -23,11 +23,11 @@ requirements: - make - {{ compiler('cxx') }} - cmake - - bamtools host: - r-base - boost - boost-cpp + - bamtools - zlib - bzip2 - r-rcpp @@ -43,6 +43,7 @@ requirements: run: - r-base - boost + - bamtools - zlib - bzip2 - r-rcpp @@ -58,6 +59,7 @@ requirements: test: commands: + - dropest --help - droptag --help - R -e "library('dropestr')" From c8cbbb3ce2d640dd7b8466a22dcc6257cf049dda Mon Sep 17 00:00:00 2001 From: vered kunik <40732104+VeredKunik@users.noreply.github.com> Date: Tue, 4 Jul 2023 15:37:30 +0300 Subject: [PATCH 65/80] Add Pedesigner (#41803) --------- Co-authored-by: Vered Kunik --- recipes/pedesigner/meta.yaml | 38 ++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 recipes/pedesigner/meta.yaml diff --git a/recipes/pedesigner/meta.yaml b/recipes/pedesigner/meta.yaml new file mode 100644 index 00000000000000..c29d3896d1bd53 --- /dev/null +++ b/recipes/pedesigner/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "pedesigner" %} +{% set version = "0.2.0" %} +{% set sha256 = "87e95b3985e087c13895243682595bcd8f051f62a5039455be2b9b3ea2c90cbc" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -vv . + +source: + url: https://github.com/VeredKunik/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - python >=3.7 + + run: + - python >=3.7 + - cas-offinder + +test: + commands: + - pedesigner --help + +about: + home: https://github.com/VeredKunik/pedesigner + license: GPL-3.0-only + license_family: GPL + summary: "A tool for prime-editing guideRNA (pegRNA) design" + +extra: + recipe-maintainers: + - VeredKunik From 1b99c95d44397a15fcd02b09457200cc9f178d38 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 07:09:50 -0600 Subject: [PATCH 66/80] Update nmrglue to 0.9 (#41361) * Update nmrglue to 0.9 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/nmrglue/meta.yaml | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/recipes/nmrglue/meta.yaml b/recipes/nmrglue/meta.yaml index 24ffb2c4fbb6ff..95067ffa1f6a00 100644 --- a/recipes/nmrglue/meta.yaml +++ b/recipes/nmrglue/meta.yaml @@ -1,13 +1,18 @@ +{% set name = "nmrglue" %} +{% set version = "0.9" %} +{% set sha256 = "be2602a08b4453bccd2b276640ebe2f06e1598aa3883492be7d11c686f623507" %} + package: - name: nmrglue - version: "0.8" + name: {{ name }} + version: {{ version }} source: - url: https://files.pythonhosted.org/packages/19/f8/75c08a1aca99471c13d20da44cbab2f4c8674de54cff249b3b2e47e5f87a/nmrglue-0.8.tar.gz - sha256: 198375ce724ab9776953a3d3ed3eb4fa0d1b859fac97360cffa5d9143f8a5bfe + url: https://files.pythonhosted.org/packages/5e/64/33f04fc1487b1606a7888c0eb75a53ddd73d83b3ed16a6dc9f6b211e2456/nmrglue-{{ version }}.tar.gz + sha256: {{ sha256 }} build: - number: 5 + number: 0 + skip: True # [py2k] script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv requirements: @@ -19,7 +24,7 @@ requirements: run: - python - numpy - - scipy <1.8.0 + - scipy test: imports: @@ -32,6 +37,7 @@ test: about: home: http://www.nmrglue.com - license: BSD License + license: BSD-3-Clause summary: 'A module for working with NMR data in Python' license_family: BSD + license_file: LICENSE.txt From 38f81b268f48ccfa0a347b6312aab12a36eea0f1 Mon Sep 17 00:00:00 2001 From: Maarten-vd-Sande Date: Tue, 4 Jul 2023 16:47:47 +0200 Subject: [PATCH 67/80] Update meta.yaml (#41829) --- recipes/seq2science/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/seq2science/meta.yaml b/recipes/seq2science/meta.yaml index 68d8a7af50c652..b25500f0c46777 100644 --- a/recipes/seq2science/meta.yaml +++ b/recipes/seq2science/meta.yaml @@ -10,7 +10,7 @@ source: build: noarch: python - number: 0 + number: 1 requirements: host: @@ -24,7 +24,7 @@ requirements: - conda =23.1.0 - mamba =1.2.0 - genomepy =0.15.0 - - biopython =1.81 + - conda-forge::biopython =1.81 - filelock =3.10.7 - pyyaml =6.0 - pandas_schema =0.3.5 From 13d1108ba05f4c5dce55d14c0de6e6d8f205bb88 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 09:54:55 -0600 Subject: [PATCH 68/80] Update annonars to 0.12.8 (#41826) --- recipes/annonars/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index 06279afd2d8795..18984e86e4d4ad 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.7" %} +{% set version = "0.12.8" %} package: name: annonars @@ -10,7 +10,7 @@ build: source: url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 769a95422791f82132aef9154d98ab15b79797baf90b299ff1a358750fd951fb + sha256: 5a1087440f0b136b2c1a4d5fb884fd2af15744831bf77636e3767ba416ed1df8 requirements: build: From 64baeddd61d0431ddc33713b87d6a49d86de721b Mon Sep 17 00:00:00 2001 From: Julianus Pfeuffer Date: Tue, 4 Jul 2023 22:25:45 +0200 Subject: [PATCH 69/80] [Update] Enable OpenMS for macOS again (#41824) * [Update] Enable OpenMS for macOS again * remove skip completely of course * remove associated comment --- recipes/openms-meta/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/openms-meta/meta.yaml b/recipes/openms-meta/meta.yaml index f53e76e83489fb..60a9477d4f4754 100644 --- a/recipes/openms-meta/meta.yaml +++ b/recipes/openms-meta/meta.yaml @@ -7,11 +7,9 @@ package: source: url: https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/{{ version }}/OpenMS-{{ version }}-src.tar.gz sha256: 2d186f35fe42573a19283605ccfb491ca6da585880fa3725a013975df26bc008 - -# osx currently skipped because of https://github.com/bioconda/bioconda-recipes/issues/41526 + build: - number: 3 - skip: True # [osx] + number: 4 # Try this when building with GUI #extra: From 112305e962914c9c25556fd6fa6effdc6d2d7f8b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 4 Jul 2023 14:28:24 -0600 Subject: [PATCH 70/80] Update tspex to 0.6.3 (#41833) --- recipes/tspex/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/tspex/meta.yaml b/recipes/tspex/meta.yaml index c4ab0e433594fb..30af6c194d4810 100644 --- a/recipes/tspex/meta.yaml +++ b/recipes/tspex/meta.yaml @@ -1,5 +1,5 @@ {% set name = "tspex" %} -{% set version = "0.6.2" %} +{% set version = "0.6.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: bb9a2ac4cc05bc7947ca57ed060ad29015f89748cfde8e9615bac26f439cc474 + sha256: 315bfa1f60ea582777c549313cad9e9da0a4d11c5f69a6fc767bd0823dc46316 build: number: 0 From 64f4f17a35b9c3a8a4a94de8ecae37a851583c40 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 06:24:06 -0600 Subject: [PATCH 71/80] Update microhapdb to 0.9 (#41818) * Update microhapdb to 0.9 * Add pyfaidx dependency * Download reference genome for test build * Fix pyfaidx pin --------- Co-authored-by: Daniel Standage --- recipes/microhapdb/meta.yaml | 5 +++-- recipes/microhapdb/run_test.sh | 2 ++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml index d88e24f7d078a5..ae8d63485b891d 100644 --- a/recipes/microhapdb/meta.yaml +++ b/recipes/microhapdb/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.8.2" %} -{% set sha256 = "d21b84765513a1229aaf796dfb4b233653ce0c8028d030db54f3396244d228ca" %} +{% set version = "0.9" %} +{% set sha256 = "ea613bdfa5a90792bb8724469966b55e012194ba49263afdafba5805c4f74d83" %} package: name: microhapdb @@ -23,6 +23,7 @@ requirements: run: - python >=3 - pandas >=1.2 + - pyfaidx >=0.7 test: imports: diff --git a/recipes/microhapdb/run_test.sh b/recipes/microhapdb/run_test.sh index 80a8ac9eb27016..16254d847a721b 100755 --- a/recipes/microhapdb/run_test.sh +++ b/recipes/microhapdb/run_test.sh @@ -1,3 +1,5 @@ #!/usr/bin/env bash set -eo pipefail +microhapdb --download pytest --cov=microhapdb --pyargs microhapdb +find $PREFIX -type f -name 'hg38*' -exec rm {} \; From 606df7c24b0e994257daeb4b4ef7f2d13e9e5387 Mon Sep 17 00:00:00 2001 From: Marc Sturm Date: Wed, 5 Jul 2023 17:40:49 +0200 Subject: [PATCH 72/80] Update ngs-bits to version 2023_06 (#41811) * Updated ngs-bits to version 2018_10 * Updated ngs-bits to version 2023_06 * updated build number * updated build command * updated build.sh * added lib path to qmake * update * update --- recipes/ngs-bits/build.sh | 2 +- recipes/ngs-bits/meta.yaml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/ngs-bits/build.sh b/recipes/ngs-bits/build.sh index 7a9bb2def6a22e..a3c73b67f42a54 100644 --- a/recipes/ngs-bits/build.sh +++ b/recipes/ngs-bits/build.sh @@ -11,7 +11,7 @@ export PATH=$BUILD_PREFIX/bin/:$PATH #build (enable debug info by adding '-Wall -d') mkdir build cd build -qmake CONFIG-=debug CONFIG+=release DEFINES+=QT_NO_DEBUG_OUTPUT QMAKE_CXX=${CXX} QMAKE_RPATHLINKDIR+=${PREFIX}/lib/ ../src/tools.pro +qmake CONFIG-=debug CONFIG+=release DEFINES+=QT_NO_DEBUG_OUTPUT QMAKE_CXX="$CXX" QMAKE_CC="$CC" QMAKE_CFLAGS="$CFLAGS" QMAKE_CXXFLAGS="$CXXFLAGS" QMAKE_LIBDIR+="$PREFIX/lib" QMAKE_RPATHLINKDIR+=${PREFIX}/lib/ ../src/tools.pro make cd .. diff --git a/recipes/ngs-bits/meta.yaml b/recipes/ngs-bits/meta.yaml index b91be72b8729c9..cbac5d063c01a8 100755 --- a/recipes/ngs-bits/meta.yaml +++ b/recipes/ngs-bits/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "2023_02" %} +{% set version = "2023_06" %} package: name: ngs-bits version: {{ version }} build: - number: 2 + number: 0 source: url: https://github.com/imgag/ngs-bits/releases/download/{{ version }}/ngs-bits-{{ version }}.tgz - sha256: 9aaf0ac7759c1f8fb3fe7f5bf84f70b235e6c25b45a3f7646f02a4b883f8d784 + sha256: 2b2583f43e9e16a98e45e670ab2d8c195f0c233abf7eaaa0c9b126d8c10d07a3 requirements: build: From c0672f71ba86b29bffd99dfc1486dd90e8a86f15 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 12:08:37 -0600 Subject: [PATCH 73/80] Update varfish-server-worker to 0.9.0 (#41846) --- recipes/varfish-server-worker/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/varfish-server-worker/meta.yaml b/recipes/varfish-server-worker/meta.yaml index 044fe8f5d3924c..f573b0e22e496a 100644 --- a/recipes/varfish-server-worker/meta.yaml +++ b/recipes/varfish-server-worker/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.8.0" %} +{% set version = "0.9.0" %} package: name: varfish-server-worker @@ -10,7 +10,7 @@ build: source: url: https://github.com/bihealth/varfish-server-worker/archive/refs/tags/v{{ version }}.tar.gz - sha256: 32dda98a4400e15a56410e5540daaa035eedfed6cf36a2fbf4516dd176b16095 + sha256: 37793ae094b01031dfd794b888547b30cc8cbf1a7dbe831a885dabde8e7f5774 requirements: build: From be6c3839eab80935b1af444e20af777b6656e687 Mon Sep 17 00:00:00 2001 From: Leonid Kostrykin Date: Wed, 5 Jul 2023 22:13:08 +0200 Subject: [PATCH 74/80] Update superdsm to 0.1.3 (#41840) * updates superdsm to 0.1.3 * retrigger build * retrigger build --- recipes/superdsm/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/superdsm/meta.yaml b/recipes/superdsm/meta.yaml index 06cb204070a992..74b82f0dfcf60d 100644 --- a/recipes/superdsm/meta.yaml +++ b/recipes/superdsm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SuperDSM" %} -{% set version = "0.1.2" %} +{% set version = "0.1.3" %} {% set repo_url = "https://github.com/BMCV/SuperDSM" %} {% set docs_url = "https://superdsm.readthedocs.io" %} @@ -9,10 +9,10 @@ package: source: url: "{{ repo_url }}/archive/refs/tags/v{{ version }}.zip" - sha256: e00e13b9bb330fccc38fb46629b651d541a3ff66339c2b5d3d962811cf375c63 + sha256: f55abbd6818a66886ddfe3f7fd9c5dd93c63ed2b6e3179552106e560a000ad5f build: - number: 1 + number: 0 noarch: python script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed . -vv " @@ -33,8 +33,7 @@ requirements: - cvxpy >=1.1.13,<2.0 - matplotlib-base >=3.0,<4.0 - mkl >=2020.0 - - posix_ipc >=1.0.4,<2.0 - - ray-default >=0.8.7 + - ray-core >=0.8.7,<1.7 test: commands: From ed820143e87d33a4674362d0efc00de2fd6b59af Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 15:42:08 -0600 Subject: [PATCH 75/80] Update pybiolib to 1.1.1073 (#41848) --- recipes/pybiolib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml index 329abb595ef222..99e5dba470d3d3 100644 --- a/recipes/pybiolib/meta.yaml +++ b/recipes/pybiolib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pybiolib" %} -{% set version = "1.1.1065" %} +{% set version = "1.1.1073" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz - sha256: 62c926afcd0a0ad7b48fd9d9a64d9449779458375a9cdebb20c26a46dfcbee8d + sha256: 880a7289c23746b4b5185c07e144bf75985f1e5b1ffbb17b8e99d14ced183a27 build: noarch: python From 95bbdcfe016ea239abc7e656c20ea58edb84c273 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 5 Jul 2023 18:01:19 -0600 Subject: [PATCH 76/80] Update gtdbtk to 2.3.2 (#41852) * Update gtdbtk to 2.3.2 * Update pydantic version. --------- Co-authored-by: Aaron Mussig --- recipes/gtdbtk/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/gtdbtk/meta.yaml b/recipes/gtdbtk/meta.yaml index 5372d2de260d55..611e22a30947f5 100644 --- a/recipes/gtdbtk/meta.yaml +++ b/recipes/gtdbtk/meta.yaml @@ -1,13 +1,13 @@ {% set name = "gtdbtk" %} -{% set version = "2.3.0" %} +{% set version = "2.3.2" %} package: name: {{ name|lower }} version: {{ version }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 4f237a03657be4540ac653c276fe31c002b6923af0411316719a9541d6e97d4b + sha256: 80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f build: - number: 2 + number: 0 noarch: python entry_points: - gtdbtk = gtdbtk.__main__:main @@ -26,7 +26,7 @@ requirements: - numpy >=1.9.0 - mash >=2.0 - tqdm >=4.35.0 - - pydantic + - pydantic >=1.9.2, <2 test: imports: - gtdbtk From df21a70589a96d5fcaf9cbd0afe3b53073f894cf Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 00:42:05 -0600 Subject: [PATCH 77/80] Update shigatyper to 2.0.5 (#41853) --- recipes/shigatyper/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/shigatyper/meta.yaml b/recipes/shigatyper/meta.yaml index 6572b27a51dff1..66642b6e2b878b 100644 --- a/recipes/shigatyper/meta.yaml +++ b/recipes/shigatyper/meta.yaml @@ -1,10 +1,10 @@ package: name: shigatyper - version: 2.0.4 + version: 2.0.5 source: - url: https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.4.tar.gz - sha256: 129a0ec7ec83bb9de6d79cf157b401fc16450a7964130c6608e1b618aa13c09d + url: https://github.com/CFSAN-Biostatistics/shigatyper/archive/refs/tags/conda-package-2.0.5.tar.gz + sha256: e853263d70bc557c7a131fac982dcd402afe3aa3fb0fc4c5fde8805b708682f1 build: noarch: python From 26d0212922e2660b249bd89e895d4250e331ca26 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 03:50:22 -0600 Subject: [PATCH 78/80] Update matchms to 0.21.1 (#41784) * Update matchms to 0.21.0 * Update matchms to 0.21.1 --- recipes/matchms/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 242f6a0423352a..99e85e308c61ff 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.20.0" %} +{% set version = "0.21.1" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: bb618eef74a23fd336b8e950ade5ecb65f1096d8ddfeced0e01934d20048557f + sha256: 9ef706361b885f8c23e14b470adb3a18fc0b156a0a243b70de8ec998a41e05ba build: number: 0 From 02d4849c0746ef344d17608224991fd8bd55d82d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 04:46:42 -0600 Subject: [PATCH 79/80] Update bioconda-utils to 2.3.3 (#41747) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update bioconda-utils to 2.3.2 * Update bioconda-utils to 2.3.3 * debug * Update meta.yaml --------- Co-authored-by: Björn Grüning Co-authored-by: Devon Ryan --- recipes/bioconda-utils/meta.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index d3f5dc49efa03f..88b92564b953e6 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.3.1" %} -{% set sha256 = "71cfdf4cfeecb2c1f2ef6b6f45c54407b6e7f0f2a8ae45fc40e51e12b36905a3" %} +{% set version = "2.3.3" %} +{% set sha256 = "aaee4e69f47d732c0e0515358a5a2b4223832a74070e751281af06c19b4dda3f" %} package: name: bioconda-utils @@ -23,7 +23,7 @@ requirements: run: - python >=3.7 - conda 23.3.* - - boa 0.14.* + - boa 0.15.* - conda-build 3.24.* - conda-verify 3.1.* - argh 0.26.* @@ -85,8 +85,7 @@ test: "${PREFIX}/bin/conda" install --prefix="${PREFIX}" --dry-run --satisfied-skip-solve --file="$( python -c 'from os.path import dirname, join; import bioconda_utils; print(join(dirname(bioconda_utils.__file__), "bioconda_utils-requirements.txt"))' - )" - 2>&1 | grep -qF 'All requested packages already installed.' + )" 2>&1 | grep -qF 'All requested packages already installed.' about: home: http://bioconda.github.io/build-system.html From bd9e3c46f797f06f3834e60401faa0e76349c83f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 6 Jul 2023 05:18:45 -0600 Subject: [PATCH 80/80] Update kallisto to 0.50.0 (#41699) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update kallisto to 0.50.0 * Update meta * Attempt to update build recipe * Include bzip2 and xz for compression handling --------- Co-authored-by: Michael Steinbaugh Co-authored-by: Johannes Köster --- recipes/kallisto/build.sh | 17 ++- recipes/kallisto/build_failure.linux-64.yaml | 104 ------------------- recipes/kallisto/build_failure.osx-64.yaml | 104 ------------------- recipes/kallisto/meta.yaml | 12 ++- 4 files changed, 16 insertions(+), 221 deletions(-) delete mode 100644 recipes/kallisto/build_failure.linux-64.yaml delete mode 100644 recipes/kallisto/build_failure.osx-64.yaml diff --git a/recipes/kallisto/build.sh b/recipes/kallisto/build.sh index 6c2dd25276e96a..b797c382d40719 100644 --- a/recipes/kallisto/build.sh +++ b/recipes/kallisto/build.sh @@ -1,15 +1,12 @@ #!/bin/bash -cd ext/htslib -autoreconf -cd ../.. - - -mkdir -p $PREFIX/bin - +cd ext/htslib || exit 1 +autoreconf --force --install --verbose +./configure +cd ../.. || exit 1 +mkdir -p "${PREFIX}/bin" mkdir -p build -cd build - -cmake -DCMAKE_INSTALL_PREFIX:PATH=$PREFIX .. -DUSE_HDF5=ON +cd build || exit 1 +cmake -DCMAKE_INSTALL_PREFIX:PATH="$PREFIX" .. -DUSE_HDF5=ON make make install diff --git a/recipes/kallisto/build_failure.linux-64.yaml b/recipes/kallisto/build_failure.linux-64.yaml deleted file mode 100644 index 65243c6acdbd7c..00000000000000 --- a/recipes/kallisto/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d2ce538a5f252b13e2bdb61ff0352bde2a0d74612792647dbafcf02a4120f347 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit - GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof - LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld - LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold - NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm - OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy - OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump - RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib - READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf - SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size - STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings - STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip - INFO: activate-gcc_linux-64.sh made the following environmental changes: - BUILD=x86_64-conda-linux-gnu - CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr - CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot - CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu - CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu - CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp - CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include - DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include - GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc - GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar - GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm - GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib - HOST=x86_64-conda-linux-gnu - LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu - build_alias=x86_64-conda-linux-gnu - host_alias=x86_64-conda-linux-gnu - -BUILD=x86_64-conda_cos6-linux-gnu - -CONDA_BUILD_SYSROOT= - INFO: activate-gxx_linux-64.sh made the following environmental changes: - CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c - DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - perl: warning: Setting locale failed. - perl: warning: Please check that your locale settings: - LANGUAGE = (unset), - LC_ALL = (unset), - LANG = "C.UTF-8" - are supported and installed on your system. - perl: warning: Falling back to the standard locale ("C"). - configure.ac: error: required file 'config.sub' not found - configure.ac: error: required file 'config.guess' not found - configure.ac: try running autoreconf --install - Traceback (most recent call last): - File "/opt/conda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/kallisto_1685523137285/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/kallisto/build_failure.osx-64.yaml b/recipes/kallisto/build_failure.osx-64.yaml deleted file mode 100644 index d9ec798831a086..00000000000000 --- a/recipes/kallisto/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: d2ce538a5f252b13e2bdb61ff0352bde2a0d74612792647dbafcf02a4120f347 # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - m4: 1.4.18-haf1e3a3_1001 conda-forge - make: 4.3-h22f3db7_1 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.1-h8a1eda9_1 conda-forge - perl: 5.32.1-2_h0d85af4_perl5 conda-forge - rhash: 1.4.3-hac89ed1_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zlib: 1.2.13-hfd90126_4 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - Downloading source to cache: v0.48.0_1797ac4d1f.tar.gz - Downloading https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: v0.48.0_1797ac4d1f.tar.gz - INFO:conda_build.source:Downloading https://github.com/pachterlab/kallisto/archive/v0.48.0.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/kallisto-0.48.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - configure.ac: error: required file 'config.sub' not found - configure.ac: error: required file 'config.guess' not found - configure.ac: try running autoreconf --install - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/kallisto_1685525877786/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index 7c058895f8de88..c312886ba195e5 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.48.0" %} +{% set version = "0.50.0" %} package: name: kallisto @@ -6,10 +6,10 @@ package: source: url: https://github.com/pachterlab/kallisto/archive/v{{ version }}.tar.gz - sha256: 1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0 + sha256: f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368 build: - number: 3 + number: 0 requirements: build: @@ -19,10 +19,14 @@ requirements: - autoconf - automake host: + - bzip2 - hdf5 + - xz - zlib run: + - bzip2 - hdf5 + - xz - zlib test: @@ -38,5 +42,7 @@ extra: identifiers: - biotools:kallisto - doi:10.1038/nbt.3519 + recipe-maintainers: + - mjsteinbaugh skip-lints: - missing_tests