Merge branch 'master' of https://github.com/bioconda/bioconda-recipes

.circleci/setup.sh

@@ -53,7 +53,6 @@ if ! type bioconda-utils 2> /dev/null || [[ $BOOTSTRAP == "true" ]]; then
     $WORKSPACE/miniconda/bin/conda config --system --add channels defaults
     $WORKSPACE/miniconda/bin/conda config --system --add channels bioconda
     $WORKSPACE/miniconda/bin/conda config --system --add channels conda-forge
-    $WORKSPACE/miniconda/bin/conda config --system --add channels conda-forge/label/cf201901
 
     # step 3: install bioconda-utils
     $WORKSPACE/miniconda/bin/conda install -y git pip --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt

build-fail-blacklist

@@ -1,3 +1,12 @@
+# Unclear that the following old versions are still needed
+recipes/hmmer/2.3.2
+recipes/bamtools/2.3.0
+recipes/bowtie/1.1.1
+recipes/fastqc/0.10.1
+recipes/fastqc/0.11.2
+recipes/fastqc/0.11.3
+recipes/fastqc/0.11.6
+
 # The build string needs to be modified to account for the [nocairo] feature
 recipes/genometools-genometools/1.5.10-nocairo
 

config.yml

@@ -7,7 +7,6 @@ blacklists:
 # of .condarc, but when adding channels using conda config --add, they should
 # be added in reverse (from low to high priority).
 channels:
-    - conda-forge/label/cf201901
     - conda-forge
     - bioconda
     - defaults

recipes/bamtools/meta.yaml

@@ -9,7 +9,7 @@ source:
   sha256: '{{sha256}}'
 
 build:
-  number: 3
+  number: 4
 
 requirements:
   build:

recipes/bcbio-nextgen-vm/meta.yaml

@@ -1,13 +1,13 @@
 package:
   name: bcbio-nextgen-vm
-  version: '0.1.2a'
+  version: '0.1.3'
 
 build:
   number: 1
 
 source:
-  url: https://github.com/bcbio/bcbio-nextgen-vm/archive/c251103.tar.gz
-  sha256: ca54003f9ec1176b769474b3db804fdaad8339330aae6bb5091ed7bb473ee944
+  url: https://github.com/bcbio/bcbio-nextgen-vm/archive/9567250.tar.gz
+  sha256: 9ce190b921105a2a208db2e1d47bc4c8e056d95ae2475af13d5e587ab8e7cc4a
 
 requirements:
   host:
@@ -25,15 +25,15 @@ requirements:
     - cachecontrol ==0.11.7
     - pathlib2 ==2.3.2
     - arvados-cwl-runner >=1.3.0.20181218191458  # [py2k and linux]
-    - cromwell >0.36
+    - cromwell >=0.36
     - ruamel.yaml >=0.13.0
     - rabix-bunny >=1.0.4
     - nodejs
     - nose
     - sbg-cwl-runner  # [py3k]
     - sevenbridges-python >=0.17.5
     - synapseclient
-    - dxpy  # [py2k]
+    - dxpy
     - dx-cwl >=0.1.0a20180820  # [py2k]
     - six
     - google-cloud-sdk

recipes/bcbio-nextgen/meta.yaml

@@ -1,14 +1,14 @@
 package:
   name: bcbio-nextgen
-  version: '1.1.3'
+  version: '1.1.4a'
 
 build:
   number: 0
 
 source:
-  url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.3.tar.gz
-  #url: https://github.com/bcbio/bcbio-nextgen/archive/c3287b5.tar.gz
-  sha256: df2e944e3a60daf33e382b1d00007d5ac1f794b2f1359c8944ade51ce59dae41
+  #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.3.tar.gz
+  url: https://github.com/bcbio/bcbio-nextgen/archive/90c156d.tar.gz
+  sha256: 32473134c2061239df554fd9764d7f60486ce86849bb0233d3deb78f5a2cc20e
 
 requirements:
   host:

recipes/bcbio-variation-recall/meta.yaml

@@ -1,12 +1,12 @@
-{% set version="0.2.1" %}
+{% set version="0.2.2" %}
 
 package:
   name: bcbio-variation-recall
   version: {{ version }}
 
 source:
   url: https://github.com/chapmanb/bcbio.variation.recall/releases/download/v{{ version }}/bcbio-variation-recall
-  sha256: fc841b2f240772f83d14d206f6831bbadd61087c7fcf56df5ff2d7607ff4e45b
+  sha256: 31258179b23dd219aa3605730cccbdff32e9cc6158da76f0afc8b9065da76040
 
 build:
   number: 0

recipes/bcftools/1.2/meta.yaml

@@ -2,7 +2,7 @@ package:
   name: bcftools
   version: "1.2"
 build:
-  number: 3
+  number: 4
 source:
   url: https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2
   md5: 8044bed8fce62f7072fc6835420f0906

recipes/bcftools/1.3.1/meta.yaml

@@ -9,7 +9,7 @@ about:
     VCF and BCF and streams will work in most, but not all situations.
 
 build:
-  number: 3
+  number: 4
 
 package:
   name: bcftools

recipes/bcftools/1.3/meta.yaml

@@ -8,7 +8,7 @@ test:
     - bcftools --version
 
 build:
-  number: 2
+  number: 3
 
 package:
   name: bcftools

recipes/bcftools/meta.yaml

@@ -10,7 +10,7 @@ about:
     VCF and BCF and streams will work in most, but not all situations.
 
 build:
-  number: 0
+  number: 1
 package:
   name: bcftools
   version: {{ version }}

recipes/bedtools/2.19.1/meta.yaml

@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

recipes/bedtools/2.20.1/meta.yaml

@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

recipes/bedtools/2.22/meta.yaml

@@ -4,7 +4,7 @@ about:
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 
 build:
-  number: 1
+  number: 2
 
 package:
   name: bedtools

recipes/bedtools/2.23.0/meta.yaml

@@ -3,7 +3,7 @@ about:
   license: 'GPL v2'
   summary: 'A swiss army knife for genome arithmetic.  https://github.com/arq5x/bedtools2 '
 build:
-  number: 1
+  number: 2
 package:
   name: bedtools
   version: '2.23.0'

recipes/bedtools/2.25/meta.yaml

@@ -7,7 +7,7 @@ source:
   sha256: d737ca42e7df76c5455d3e6e0562cdcb62336830eaad290fd4133a328a1ddacc
 
 build:
-  number: 4
+  number: 5
 
 requirements:
   build:

recipes/bedtools/2.26.0/meta.yaml

@@ -9,7 +9,7 @@ source:
     - 2.26.0_postrelease.patch
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

recipes/bedtools/2.27.0/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

recipes/bedtools/2.27.1/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: c8c2acbaf3f9cb92dcf8e5cd59af6b31ae9c4598efb786ba6c84f66ca72fafd9
 
 build:
-  number: 2
+  number: 3
 
 requirements:
   build:

recipes/biobb_analysis/build.sh

@@ -2,6 +2,8 @@
 
 python3 setup.py install --single-version-externally-managed --record=record.txt
 
+conda install -c ambermd ambertools 
+
 mkdir -p $PREFIX/bin
 
 chmod u+x $SP_DIR/biobb_analysis/gromacs/rms.py

recipes/biobb_analysis/meta.yaml

@@ -20,14 +20,12 @@ requirements:
   host:
     - python >=3
     - setuptools
-    - biobb_common >=0.0.8
-    - biopython
+    - biobb_common >=0.1.2
+    - gromacs >=2018.4
   run:
     - python >=3
-    - biobb_common >=0.0.8
-    - biopython
-
-
+    - biobb_common >=0.1.2
+    - gromacs >=2018.4
 test:
   imports:
     - biobb_analysis
@@ -40,12 +38,12 @@ about:
   license_family: APACHE
   license_file: ''
   summary: Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
-  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/159c05eeeb094019b4ef0b4ab000d566)](https://www.codacy.com/app/andriopau/biobb_analysis?utm_source=github.com&utm_medium=referral&utm_content=bioexcel/biobb_analysis&utm_campaign=Badge_Grade)\n\
+  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest)\n\
     \n# biobb_analysis\n\n### Introduction\nBiobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\
-    \n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\
-    \ (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018\
-    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
+    \n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\
+    \ (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2019\
+    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2019 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
     \ see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
   doc_url: ''
   dev_url: ''

recipes/biobb_common/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "biobb_common" %}
-{% set version = "0.0.8" %}
+{% set version = "0.1.2" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "58e2babcf9c1523bff2d673c7b62df425517ddf17966cf3145873841706343e2" %}
+{% set hash_value = "f3be96dc9923c1cbb6cf4a67f9f2a5d78ad8ccbef389c2025dc38ca414e00c1b" %}
 
 package:
   name: '{{ name|lower }}'
@@ -22,12 +22,12 @@ requirements:
     - setuptools
     - pyyaml
     - requests
-    - biopython
+    - biopython >=1.72
   run:
     - python >=3
     - pyyaml
     - requests
-    - biopython
+    - biopython >=1.72
 
 test:
   imports:
@@ -42,12 +42,12 @@ about:
   license_family: APACHE
   license_file: ''
   summary: Biobb_common is the base package required to use the biobb packages.
-  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-common/badge/?version=latest)](https://biobb-common.readthedocs.io/en/latest/?badge=latest)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/8e5c5537c6234bff958171e273471879)](https://www.codacy.com/app/andriopau/biobb_common?utm_source=github.com&utm_medium=referral&utm_content=bioexcel/biobb_common&utm_campaign=Badge_Grade)\n\
+  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-common/badge/?version=latest)](https://biobb-common.readthedocs.io/en/latest/?badge=latest)\n\
     \n# biobb_common\n\n### Introduction\nBiobb_common is the base package required to use the biobb\npackages.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate new layer\
     \ of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).\n\
-    \n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/)\
-    \ & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018\
-    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
+    \n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/)\
+    \ & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2019\
+    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2019 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
     \ see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
   doc_url: ''
   dev_url: ''

recipes/biobb_io/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "biobb_io" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.3" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "b1d85c970bebce1c9c7c62a9e7e469a337c33aeb22083bf8e23f506e93b57b08" %}
+{% set hash_value = "2314b417958b80c44107e6da5de9e53f5dbe8b364a1560b0b80cb8eca0f10539" %}
 
 package:
   name: '{{ name|lower }}'
@@ -20,13 +20,10 @@ requirements:
   host:
     - python >=3
     - setuptools
-    - biobb_common >=0.0.8
-    - requests
+    - biobb_common >=0.1.2
   run:
     - python >=3
-    - biobb_common >=0.0.8
-    - requests
-
+    - biobb_common >=0.1.2
 test:
   imports:
     - biobb_io
@@ -38,12 +35,12 @@ about:
   license_family: APACHE
   license_file: ''
   summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
-  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-io/badge/?version=latest)](https://biobb-io.readthedocs.io/en/latest/?badge=latest)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/f98ed1286f244616bf39352e1877d310)](https://www.codacy.com/app/andriopau/biobb_io?utm_source=github.com&utm_medium=referral&utm_content=bioexcel/biobb_io&utm_campaign=Badge_Grade)\n\
+  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-io/badge/?version=latest)](https://biobb-io.readthedocs.io/en/latest/?badge=latest)\n\
     \n# biobb_io\n\n### Introduction\nBiobb_io is the Biobb module collection to fetch data to be consumed by the\nrest of the Biobb building blocks.\nBiobb (BioExcel building blocks) packages are Python\
     \ building blocks that\ncreate new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest\
-    \ API documentation](http://biobb_io.readthedocs.io/en/latest/).\n\n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org)\
+    \ API documentation](http://biobb_io.readthedocs.io/en/latest/).\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org)\
     \ at the\nBSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\
-    \n* (c) 2015-2018 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License\
+    \n* (c) 2015-2019 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2019 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License\
     \ 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
   doc_url: ''
   dev_url: ''

recipes/biobb_md/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "biobb_md" %}
-{% set version = "0.1.2" %}
+{% set version = "0.1.4" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "e6c13d971d93635860742c7fb13d62c0debb2208b0577cd39e289dee7546ad1e" %}
+{% set hash_value = "d364e8f0b7d960e64f8042f9ec14b418cad7d37f00ac4ef93c7bc2de8f21d771" %}
 
 package:
   name: '{{ name|lower }}'
@@ -20,14 +20,12 @@ requirements:
   host:
     - python >=3
     - setuptools
-    - biobb_common >=0.0.8
-    - biopython
+    - biobb_common >=0.1.2
+    - gromacs >=2018.4
   run:
     - python >=3
-    - biobb_common >=0.0.8
-    - biopython
-
-
+    - biobb_common >=0.1.2
+    - gromacs >=2018.4
 test:
   imports:
     - biobb_md
@@ -40,12 +38,12 @@ about:
   license_family: APACHE
   license_file: ''
   summary: Biobb_md is the Biobb module collection to perform molecular dynamics simulations.
-  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-md/badge/?version=latest)](https://biobb-md.readthedocs.io/en/latest/?badge=latest)\n[![Codacy Badge](https://api.codacy.com/project/badge/Grade/159c05eeeb094019b4ef0b4ab000d566)](https://www.codacy.com/app/andriopau/biobb_md?utm_source=github.com&utm_medium=referral&utm_content=bioexcel/biobb_md&utm_campaign=Badge_Grade)\n\
+  description: "[![Documentation Status](https://readthedocs.org/projects/biobb-md/badge/?version=latest)](https://biobb-md.readthedocs.io/en/latest/?badge=latest)\n\
     \n# biobb_md\n\n### Introduction\nBiobb_md is the Biobb module collection to perform molecular dynamics simulations.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_md.readthedocs.io/en/latest/).\n\
-    \n### Version\nThis software is in Alpha version.\n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\
-    \ (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2018\
-    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2018 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
+    \n\n### Copyright & Licensing\nThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the\nBSC (http://www.bsc.es/) & IRB\
+    \ (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission\n(EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\n\n* (c) 2015-2019\
+    \ [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2019 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\nLicensed under the\n[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0),\
     \ see the file\n[LICENSE](LICENSE) for details.\n\n![](https://bioexcel.eu/wp-content/uploads/2015/12/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
   doc_url: ''
   dev_url: ''