Merge branch 'bioconda:master' into master

recipes/abromics_galaxy_json_extractor/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.5" %}
+{% set version = "0.6" %}
 
 context: {}
 
@@ -8,7 +8,7 @@ package:
 
 source:
   url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz
-  sha256:  '39b6c39c878eefc975a414c3170a83a33c017ae8b741a46ff905f3e81ba1f952'
+  sha256:  '8ba4bde77817fa323e279a6f2e8187e364259a7e69b92c11f02ba5332eeeb950'
 
 build:
   noarch: python

recipes/agat/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "AGAT" %}
-{% set version = "1.1.0" %}
-{% set sha256 = "38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002" %}
+{% set version = "1.2.0" %}
+{% set sha256 = "c812e4b4ca1d27b5b8804025fa5a33f56e9b542948b44885662b2cbb98d06055" %}
 
 package:
   name: "{{ name|lower }}"
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 1
+  number: 0
 
 requirements:
   host:

recipes/annonars/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.12.9" %}
+{% set version = "0.13.0" %}
 
 package:
   name: annonars
@@ -10,7 +10,7 @@ build:
 
 source:
   url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 6e1869f4965bd096b60c386253f6a85879094ad50b01541c6df04f8225f87cdc
+  sha256: ff578294324da4445381a9a55ea03969cf8665dc008384879919ded6169c4772
 
 requirements:
   build:
@@ -37,8 +37,8 @@ test:
 about:
   home: https://github.com/bihealth/annonars
   license: Apache-2.0
-  summary: |
-     Genome annotation based on Rust and RocksDB.
+  license_file: LICENSE.txt
+  summary: 'Genome annotation based on Rust and RocksDB.'
 
 extra:
   recipe-maintainers:

recipes/bayescode/build.sh

@@ -1,12 +1,28 @@
 #!/bin/bash
-
+rm -rf data/
+# Build specifying CPP compiler and C compiler
+# Use sed to replace 'make' with 'make CXX=${CXX} CC=${CC}'
+# This is necessary because the Makefile does not respect the CXX and CC variables
 # Create bin directory
+mkdir bin
 mkdir -p "${PREFIX}"/bin/
+mv utils/*.py "${PREFIX}"/bin/
+
+# Generate Makefile
+cd bin; cmake -DTINY=ON ..
+
+# Build executables mutselomega and readmutselomega
+make CXX=${GXX} CC=${CC} -j ${CPU_COUNT} mutselomega readmutselomega
+mv mutselomega "${PREFIX}"/bin/; mv readmutselomega "${PREFIX}"/bin/
+
+# Build executables nodemutsel and readnodemutsel
+make CXX=${GXX} CC=${CC} -j ${CPU_COUNT} nodemutsel readnodemutsel
+mv nodemutsel "${PREFIX}"/bin/; mv readnodemutsel "${PREFIX}"/bin/
 
-# Build PSASS specifying CPP compiler and C compiler
-make CXX="${CXX}" CC="${CC}" tiny
+# Build executables nodeomega and readnodeomega
+make CXX=${GXX} CC=${CC} -j ${CPU_COUNT} nodeomega readnodeomega
+mv nodeomega "${PREFIX}"/bin/; mv readnodeomega "${PREFIX}"/bin/
 
-# Copy all generated binaries to bin
-cp bin/*mutselomega "${PREFIX}"/bin/
-cp bin/*nodemutsel "${PREFIX}"/bin/
-cp utils/*.py "${PREFIX}"/bin
+# Build executables nodetraits and readnodetraits
+make CXX=${GXX} CC=${CC} -j ${CPU_COUNT} nodetraits readnodetraits
+mv nodetraits "${PREFIX}"/bin/; mv readnodetraits "${PREFIX}"/bin/

recipes/bayescode/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "1.1.6" %}
-{% set sha256 = "de135fc290f61ff3fb73526742d55effe84c2d25511a7454a7f7dfb48f6415ef" %}
+{% set version = "1.2.2" %}
+{% set sha256 = "cd60df1166d05cd0107ba8da61de42d038dfb2c5514af2f57ee12f9788c947af" %}
 
 package:
   name: bayescode
   version: {{ version }} 
 
 build:
-  number: 2
+  number: 0
 
 source:
   url: https://github.com/ThibaultLatrille/bayescode/archive/refs/tags/v{{ version }}.tar.gz
@@ -16,8 +16,8 @@ requirements:
   build:
     - make
     - cmake
-    - {{ compiler('cxx') }}
     - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
   host:
   run:
     - python >=3.6
@@ -32,10 +32,15 @@ test:
     - calibs_coevol_to_mutsel.py --help
     - traits_coevol_to_mutsel.py --help
     - plot_tree.py --help
+    - neutrality_index.py --help
     - mutselomega --help
     - readmutselomega --help
     - nodemutsel --help
     - readnodemutsel --help
+    - nodeomega --help
+    - readnodeomega --help
+    - nodetraits --help
+    - readnodetraits --help
 
 about:
   home: https://github.com/ThibaultLatrille/bayescode

recipes/beav/build.sh

@@ -9,12 +9,12 @@ mkdir -p $BEAV_DIR/models
 mkdir -p $BEAV_DIR/test_data
 mkdir -p $PREFIX/bin
 
-cp beav $PREFIX/bin
-cp beav_db $PREFIX/bin
-cp -r scripts/* $BEAV_DIR/scripts
-cp -r databases/* $BEAV_DIR/databases
-cp -r models/* $BEAV_DIR/models
-cp -r test_data/* $BEAV_DIR/test_data
+mv beav $PREFIX/bin
+mv beav_db $PREFIX/bin
+mv scripts/* $BEAV_DIR/scripts
+mv databases/* $BEAV_DIR/databases
+mv models/* $BEAV_DIR/models
+mv test_data/* $BEAV_DIR/test_data
 
 git clone https://github.com/weisberglab/DBSCAN-SWA $BEAV_DIR/software/DBSCAN-SWA
 
@@ -24,7 +24,7 @@ mkdir $BEAV_DIR/software/PaperBLAST/bin/blast
 #TIGER
 curl -v -L -O https://github.com/sandialabs/TIGER/archive/refs/tags/TIGER2.1.tar.gz
 tar xzf TIGER2.1.tar.gz --exclude 'TIGER-TIGER2.1/db/Pfam-A.hmm' --exclude 'TIGER-TIGER2.1/bin/aragorn*' --exclude 'TIGER-TIGER2.1/bin/hmmsearch' --exclude 'TIGER-TIGER2.1/bin/pfscan'
-patch -p 0 -d ./ < scripts/tiger.patch
+patch -p 0 -d ./ < $BEAV_DIR/scripts/tiger.patch
 mv TIGER-TIGER2.1 $BEAV_DIR/software/TIGER
 rm TIGER2.1.tar.gz
 

recipes/beav/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "beav" %}
-{% set version = "0.2" %}
-{% set sha256 = "104324a35c36d886d17423d0e81378ce24a120a3bbaf2a45e73dd7ff619aaeff" %}
+{% set version = "0.4.5" %}
+{% set sha256 = "dfb8b6fcd99834c631a509ba6214dda2f21d828e932d9d64dc7f1444b7e699f0" %}
 
 package:
   name: {{ name }}

recipes/biobb_analysis/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_analysis" %}
-{% set version = "4.0.1" %}
+{% set version = "4.0.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 65c36326ab0f4223d6f53ed1730ab29867d7b086f9d439a029f9822a971a4ddb
+  sha256: 455757f0292214ead650b4735c5a77010125e326f1e5c601f671331d4e725a9a
 
 build:
   number: 0

recipes/biobb_flexserv/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_flexserv" %}
-{% set version = "4.0.2" %}
+{% set version = "4.0.3" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: cd6257fa189c2b83a33c40a4f37dadf70638f66fb206bdb832d5fe262ea12819 
+  sha256: 8754c5050281fd07c5c7797de5d91a8d741b6658ad260752e0582959ff4afc14 
 
 build:
   number: 0

recipes/biobb_godmd/meta.yaml

@@ -1,29 +1,29 @@
 {% set name = "biobb_godmd" %}
-{% set version = "4.0.0" %}
+{% set version = "4.0.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 495b6bb47aa77b312e1b34514dc0ea64b5229676c23e9104b521e4ba34611602 
+  sha256: 170e82621f501dc9d624ac6a324936dfb90b38e55dece06f64495ab5c1fd504f 
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
 
 requirements:
   host:
-    - python >=3.7,<=3.10
+    - python >=3.7,<3.10
     - setuptools
     - biobb_common ==4.0.0
     - godmd ==1.0.0
     - emboss
 
   run:
-    - python >=3.7,<=3.10
+    - python >=3.7,<3.10
     - biobb_common ==4.0.0
     - godmd ==1.0.0
     - emboss

recipes/biobb_structure_utils/meta.yaml

@@ -10,21 +10,21 @@ source:
   sha256: 1ca56a2d12600b057bd3d6db514a1edc38bb72f8a2de106bc696169463dd9b79
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
 
 
 requirements:
   host:
-    - python >=3.7,<=3.10
+    - python >=3.7,<3.10
     - setuptools
     - biobb_common ==4.0.0
-    - biobb_structure_checking ==3.12.1
+    - biobb_structure_checking ==3.13.0
   run:
-    - python >=3.7,<=3.10
+    - python >=3.7,<3.10
     - biobb_common ==4.0.0
-    - biobb_structure_checking ==3.12.1
+    - biobb_structure_checking ==3.13.0
 test:
   imports:
     - biobb_structure_utils

recipes/bioconductor-affy/meta.yaml

@@ -13,30 +13,38 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 1b3ca024b5fc6804d66023f11c058955
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
 # Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
 requirements:
   host:
     - 'bioconductor-affyio >=1.70.0,<1.71.0'
+    - bioconductor-annotationdbi
     - 'bioconductor-biobase >=2.60.0,<2.61.0'
     - 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
     - 'bioconductor-preprocesscore >=1.62.0,<1.63.0'
     - 'bioconductor-zlibbioc >=1.46.0,<1.47.0'
     - r-base
     - r-biocmanager
+    - r-curl
+    - r-plogr
+    - r-rsqlite
     - libblas
     - liblapack
   run:
     - 'bioconductor-affyio >=1.70.0,<1.71.0'
+    - bioconductor-annotationdbi
     - 'bioconductor-biobase >=2.60.0,<2.61.0'
     - 'bioconductor-biocgenerics >=0.46.0,<0.47.0'
     - 'bioconductor-preprocesscore >=1.62.0,<1.63.0'
     - 'bioconductor-zlibbioc >=1.46.0,<1.47.0'
     - r-base
     - r-biocmanager
+    - r-curl
+    - r-plogr
+    - r-rsqlite
   build:
     - {{ compiler('c') }}
     - automake