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Merge branch 'master' into fix-pgscatalog-utils
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nebfield authored Oct 8, 2024
2 parents 8deeb72 + 77e9015 commit 2d4321c
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1 change: 0 additions & 1 deletion build-fail-blacklist
Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,6 @@ recipes/gemma
recipes/roary
recipes/deltabs
recipes/gottcha
recipes/pepnovo
recipes/ea-utils
recipes/nextgenmap
recipes/igor_vdj
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4 changes: 2 additions & 2 deletions recipes/bactopia-py/meta.yaml
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@@ -1,13 +1,13 @@
{% set name = "bactopia-py" %}
{% set version = "1.2.0" %}
{% set version = "1.2.1" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
sha256: 0981bd53baba2318dbd3cdf4071f0a735e85ec65a2c005181f10866d522c1fef
sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1

build:
noarch: python
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15 changes: 13 additions & 2 deletions recipes/breseq/build.sh
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@@ -1,5 +1,16 @@
#!/bin/bash

set -eux
./configure --prefix=$PREFIX
make -j ${CPU_COUNT}

export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export M4="${BUILD_PREFIX}/bin/m4"

autoreconf -if
./configure --prefix="${PREFIX}" \
CXX="${CXX}" \
CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
LDFLAGS="${LDFLAGS}"
make -j "${CPU_COUNT}"
make install
17 changes: 12 additions & 5 deletions recipes/breseq/meta.yaml
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Expand Up @@ -9,19 +9,20 @@ source:
sha256: "39b35e246ecd2b497c82a99765ca4d78a0400bc4a7518b7506b140229ccc0247"

build:
number: 1
number: 2
run_exports:
- {{ pin_subpackage('breseq', max_pin="x.x") }}

requirements:
build:
- make
- {{ compiler("c") }}
- {{ compiler("cxx") }}
- autoconf
- automake
- libtool
host:
- zlib
run:
- zlib
- r-base
- r-cairo
- bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1
Expand All @@ -36,11 +37,17 @@ about:
license: GPL-2.0-or-later
license_family: GPL
license_file: COPYING
summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
data.
summary: "A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
data."
doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/"
dev_url: https://github.com/barricklab/breseq

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:breseq
- biotools:breseq_bam2aln
- biotools:breseq_bam2cov
- usegalaxy-eu:breseq
4 changes: 2 additions & 2 deletions recipes/civicpy/meta.yaml
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@@ -1,13 +1,13 @@
{% set name = "civicpy" %}
{% set version = "3.1.0" %}
{% set version = "3.1.1" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
sha256: 1e9d5a36dff490c5a806cfc152c5f998ba13a54e409cb72eff392dc2ada14537
sha256: c67960193aae89ca69a1e102bbc8af1fc34ff1007dbc41525514dec7bb9b14c7

build:
number: 0
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4 changes: 2 additions & 2 deletions recipes/dajin2/meta.yaml
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@@ -1,13 +1,13 @@
{% set name = "DAJIN2" %}
{% set version = "0.5.4" %}
{% set version = "0.5.5" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/dajin2-{{ version }}.tar.gz
sha256: c90d026e219c93bd7211d00fabd4e8e5ee0c145e9fc5f0b4ddbd6a72281abe35
sha256: c0260f99ad631b505b0f0fa010ce7b3ef2f081bcb371ed452bd886dd34592ac1

build:
entry_points:
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3 changes: 2 additions & 1 deletion recipes/fastaptamer/build.sh
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@@ -1,3 +1,4 @@
#!/bin/bash

mkdir -p ${PREFIX}/bin
cp fastaptamer_* $PREFIX/bin
cp -rf fastaptamer_* $PREFIX/bin
13 changes: 8 additions & 5 deletions recipes/fastaptamer/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
{% set version = "1.0.14" %}
{% set version = "1.0.16" %}

package:
name: fastaptamer
version: {{ version }}

source:
url: https://github.com/FASTAptamer/FASTAptamer/archive/v{{ version }}.tar.gz
sha256: 261ffd8364fef68a762a94851da6b0e5969e44bafab1a91033afc5499532b446
sha256: 8333a6d96a4bb44ca45f4f37af10613c5a04e73a83ec1648612c43e383a9140d

build:
number: 1
number: 0
noarch: generic
run_exports:
- {{ pin_subpackage('fastaptamer', max_pin="x") }}

requirements:
run:
Expand All @@ -21,7 +23,8 @@ test:
- fastaptamer_cluster -h

about:
home: http://burkelab.missouri.edu/fastaptamer.html
license: GNU General Public License v3.0
home: https://burkelab.missouri.edu/fastaptamer.html
license: "GPL-3.0-or-later"
license_family: GPL3
license_file: LICENSE.txt
summary: A Bioinformatic Toolkit for High-Throughput Sequence Analysis of Combinatorial Selections
9 changes: 0 additions & 9 deletions recipes/galaxy_sequence_utils/build.sh

This file was deleted.

24 changes: 13 additions & 11 deletions recipes/galaxy_sequence_utils/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "galaxy_sequence_utils" %}
{% set version = "1.1.5" %}
{% set sha256 = "c32bd91f6ff11ad6e8b62f8de309d695ef5c33a782afbf5122c1db7144ef1162" %}
{% set version = "1.2.0" %}
{% set sha256 = "103f0e25f5660793253d9ac540c2eb2d7ddc82d16aa0a62c0869b60033898410" %}

package:
name: {{ name|lower }}
Expand All @@ -13,13 +13,13 @@ about:
summary: Sequence Utilities from the Galaxy project

source:
url: https://pypi.io/packages/source/g/galaxy-sequence-utils/galaxy_sequence_utils-{{ version }}.tar.gz
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/galaxy_sequence_utils-{{ version }}.tar.gz
sha256: {{ sha256 }}

build:
noarch: python
number: 2
preserve_egg_dir: True
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
run_exports:
-{{ pin_subpackage(name, max_pin="x") }}
entry_points:
Expand All @@ -40,18 +40,20 @@ build:

requirements:
host:
# uses the imp module which has been deprecated in 3.12
- python <3.12
- python >=3.8
- setuptools
- six

- pip
run:
- python <3.12
- six
- python >=3.8

test:
imports:
- galaxy_utils
commands:
- gx-fastq-groomer --help
- gx-fastq-trimmer-by-quality --help
- gx-fastq-masker-by-quality --help

extra:
recipe-maintainers:
- nsoranzo
6 changes: 3 additions & 3 deletions recipes/gfastats/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{% set name = "gfastats" %}
{% set version = "1.3.7" %}
{% set version = "1.3.8" %}

package:
name: {{ name }}
version: {{ version }}
Expand All @@ -10,7 +10,7 @@ source:
git_tag: v{{ version }}

build:
number: 1
number: 0
run_exports:
- {{ pin_subpackage('gfastats', max_pin="x") }}

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69 changes: 69 additions & 0 deletions recipes/gsmap/meta.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
{% set name = "gsmap" %}
{% set version = "1.70" %}

package:
name: {{ name }}
version: {{ version }}

source:
url: "https://pypi.io/packages/source/{{ name[0] }}/gsMap/{{ name }}-{{ version }}.tar.gz"
sha256: 54a8373c79c1ffe71e0b4c1e2cf33aed1a61b742e23efa05b00b8466b3ec3da9

build:
noarch: python
number: 0
script: {{ PYTHON }} -m pip install . --no-deps -vv
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}

requirements:
host:
- python >=3.8
- pip
- flit >=3.2,<4

run:
- python >=3.8
- numpy
- pandas
- scipy
- scikit-learn
- matplotlib-base
- seaborn
- tqdm
- progress
- pyyaml
- pyranges
- pyfiglet
- plotly
- kaleido-core
- jinja2
- scanpy >=1.8
- zarr
- bitarray
- pyarrow
- scikit-misc

test:
commands:
- gsmap --help

about:
home: https://github.com/LeonSong1995/gsMap
license: MIT
license_file: LICENSE
summary: "gsMap (genetically informed spatial mapping of cells for complex traits)"
description: |
gsMap integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
authors:
- name: liyang
email: songliyang@westlake.edu.cn
- name: wenhao
email: chenwenhao@westlake.edu.cn
doc_url: "https://yanglab.westlake.edu.cn/gsmap/document"
dev_url: "https://github.com/LeonSong1995/gsMap"

extra:
recipe-maintainers:
- Ganten-Hornby
- leonSong1995
4 changes: 2 additions & 2 deletions recipes/gtotree/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
{% set name = "GToTree" %}
{% set version = "1.8.7" %}
{% set version = "1.8.8" %}

package:
name: "{{ name|lower }}"
version: "{{ version }}"

source:
url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz
sha256: 2ec94fa0bbcfa98edca126ee3446ab7fa8982cd746604b371f74a125e3e44435
sha256: 81e5856fa188a5096725605a31a1bf6bf4f8baa1dc2acc83eda29a0ff7a742b5

build:
number: 0
Expand Down
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