Merge branch 'master' into bump/lotus2

bioconda · Jul 6, 2023 · 07ff315 · 07ff315
2 parents dc411de + bd9e3c4
commit 07ff315
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diff --git 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:

diff --git 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
@@ -10,22 +10,22 @@ build:
 
 source:
   url: https://github.com/bactopia/bactopia-gather/archive/v{{version}}.tar.gz
-  sha256: e8973fc58ef004803944bdf31ff47cd0acbf3665656f0f45044c0efd96680408
+  sha256: a8fb55e78a723f2ff239a2f6e254cccbd38283321b483220622f77c13c82fe9f
 
 requirements:
   run:
     - art >=2016.06.05
     - 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
 

diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bactopia-py" %}
-{% set version = "1.0.3" %}
+{% set version = "1.0.4" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
-  sha256: ddbd5a4e776ef4a958ceec5bd0e017323a380417420d27ebf9e1cde708104d15
+  sha256: c139be0d812f95cf466347ca03f1b4875e2f64038b5c5aec3f33dc438c4a195f
 
 build:
   noarch: python

diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.1.1" %}
+{% set version = "1.2.0" %}
 
 package:
   name: bioblend
   version: {{ version }}
 
 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

diff --git 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

diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml
@@ -1,15 +1,15 @@
-{% set version = "0.42.0" %}
+{% set version = "0.43.0" %}
 
 package:
   name: bustools
   version: {{ version }}
 
 source:
   url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz
-  sha256: 34027724b9c57bdbf2e7c252962e30c329b3f5f9fc03d10a5feef336ce50d008
+  sha256: a881fd273e4242a422a60e69b2d47210880fba855346a13efbc5480e7a2f9721
 
 build:
-  number: 2
+  number: 0
 
 requirements:
   build:

diff --git a/recipes/checkqc/meta.yaml b/recipes/checkqc/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "checkQC" %}
-{% set version = "3.8.0" %}
+{% set version = "3.8.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 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
 

diff --git a/recipes/cwltest/meta.yaml b/recipes/cwltest/meta.yaml
diff --git a/recipes/decoupler/meta.yaml 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
diff --git a/recipes/deepfplearn/meta.yaml 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.
+
diff --git 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')"
 

diff --git 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
diff --git a/recipes/fastqe/meta.yaml b/recipes/fastqe/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "fastqe" %}
-{% set version = "0.2.7" %}
+{% set version = "0.3.1" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 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
@@ -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',