Merge remote-tracking branch 'origin/master'

bioconda · Sep 26, 2024 · 293e042 · 293e042
2 parents 6041af8 + db60b4b
commit 293e042
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diff --git a/recipes/abnumber/meta.yaml b/recipes/abnumber/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "0.3.8" %} # Remember to update sha256 below
+{% set version = "0.4.1" %} # Remember to update sha256 below
 
 package:
   name: abnumber
   version: '{{ version }}'
 
 source:
   url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz
-  sha256: '9d811615800d479bb2ddd54996f1255806bd9ebc140407a54a0bc1790f9a8cee'
+  sha256: '240c7ccc1f85607ffdd0109f19761ab0488a059ae15e3ccd6066ef36c192a047'
 
 build:
   noarch: python

diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml
@@ -1,22 +1,22 @@
 {% set name="ampliconsuite" %}
-{% set AS_version="1.3.3" %}
+{% set AS_version="1.3.4" %}
 {% set AA_version="1.4.r2" %}
-{% set AC_version="1.2.0" %}
+{% set AC_version="1.2.1" %}
 
 package:
     name: {{ name }}
     version: {{ AS_version }}
 
 source:
-    # the sha256 sum is generated by doing
+    # the sha256 sum is generated by running the following on the release .tar.gz from Github.
     # $ wget -O- [URL] | shasum -a 256
     - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
-      sha256: c29f159cb641068b5c38529eeb49a975d63b3369407603cf30f3d8cf49a380d5
+      sha256: 58f2b74eac0116e0830bceea66a854071e2a205b6f5b8e57ce61a0e358434a61
     - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
       sha256: 987390d7a32a6c118e6c7fea5c7a5aba2db1b3e64fc3ece5f68f50c7cabf01fa
       folder: ampliconarchitectlib
     - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
-      sha256: 85052324376756ca3558325dce45635276af3f41dd292601f673abaf9990790a
+      sha256: 5cd6b9f4e2239631b8f11adda99d8858c29de64cf6f1c7a38121946db06803c9
 
 build:
     noarch: python

diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.2.8" %}
-{% set sha256 = "f7f67b6c01d3840376a4da89b9157cacea77eda2b078a4aa6502403b3fd8dffd" %}
+{% set version = "1.2.9" %}
+{% set sha256 = "084aec699f266e21b457db2cb86c75d73e29b071bdd837cb987561942aa01510" %}
 
 package:
   name: delly

diff --git a/recipes/earlgrey/build.sh b/recipes/earlgrey/build.sh
@@ -26,10 +26,10 @@ cd ../ && rm -rf SA-SSR/
 
 # Fixes to earlGrey executable
 sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGrey  #remove check that conda environment has a specific name
-
+sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyLibConstruct  #remove check that conda environment has a specific name
 
 # Fixes sed command for executables so that it works on both linux and macos
-sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
+sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${PACKAGE_HOME}/earlGreyLibConstruct ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
 
 # Remove -pa from RepeatClassifier
@@ -43,6 +43,7 @@ sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer
 
 # Add SCRIPT_DIR to correct path
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGrey
+sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGreyLibConstruct
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/rcMergeRepeat*
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/headSwap.sh
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/autoPie.sh
@@ -51,6 +52,7 @@ sed -i.bak "s|INSERT_FILENAME_HERE|${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT
 
 # Set permissions to files
 chmod +x ${PACKAGE_HOME}/earlGrey
+chmod +x ${PACKAGE_HOME}/earlGreyLibConstruct
 chmod +x ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 chmod +x ${SCRIPT_DIR}/* > /dev/null 2>&1
 chmod +x ${SCRIPT_DIR}/bin/LTR_FINDER.x86_64-1.0.7/ltr_finder
@@ -76,3 +78,4 @@ echo "unset PERL5LIB" >> "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivat
 # Put earlGrey executable in bin
 cd ${PREFIX}/bin
 ln -sf ${PACKAGE_HOME}/earlGrey .
+ln -sf ${PACKAGE_HOME}/earlGreyLibConstruct .
diff --git a/recipes/earlgrey/meta.yaml b/recipes/earlgrey/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('earlgrey', max_pin='x') }}
 

diff --git a/recipes/ena-upload-cli/meta.yaml b/recipes/ena-upload-cli/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "ena-upload-cli" %}
-{% set version = "0.7.3" %}
+{% set version = "0.7.4" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/usegalaxy-eu/ena-upload-cli/archive/refs/tags/{{ version }}.tar.gz"
-  sha256: 9508f63fddb0dc9541f1500e0c4ed064c21ad59ac3e0d2140497475387113745
+  sha256: da6b07a681ae6c9ac61ca5b3e7e6fe8a5ed3f0ed7bae64936e19b33dfb2782bc
 
 build:
   number: 0
@@ -26,7 +26,7 @@ requirements:
     - genshi ==0.7.*
     - lxml >=4.9.3,<=5.0.0
     - pandas >=2.0.3,<=3.0.0
-    - pyyaml ==5.*
+    - pyyaml ==5.3.*
     - requests >=2.31.0,<=3.0.0
     - openpyxl >=3.1.2,<=4.0.0
     - jsonschema >=4.19.1

diff --git a/recipes/falco/build.sh b/recipes/falco/build.sh
@@ -7,16 +7,22 @@ export M4="$BUILD_PREFIX/bin/m4"
 # add Configuration and example files to opt
 falco=$PREFIX/opt/falco
 mkdir -p $falco
-cp -r ./* $falco
+cp -rf ./* $falco
 
 #to fix problems with htslib
 export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include
 export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${PREFIX}/include
 export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
 export LD_LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
 
+export INCLUDES="-I{PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include"
+
 cd $falco
-./configure --prefix=$falco --enable-hts
+autoreconf -if
+./configure --prefix=$falco --enable-hts CXX="${CXX}" CXXFLAGS="${CXXFLAGS}"
 make -j ${CPU_COUNT}
 make install
 for i in $(ls -1 | grep -v Configuration | grep -v bin);

diff --git a/recipes/falco/meta.yaml b/recipes/falco/meta.yaml
@@ -1,40 +1,41 @@
-{% set version = "1.2.3" %}
+{% set version = "1.2.4" %}
 
 package:
   name: falco
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     # falco is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('falco', max_pin="x.x") }}
 
-
 source:
   url: https://github.com/smithlabcode/falco/releases/download/v{{ version }}/falco-{{ version }}.tar.gz
-  sha256: b2d4da736efecfa669ad555fbb69862bc7fb57dcf32efcb6c151c47f98b32b8a
+  sha256: 116c257fbf87bf99083d8e539a51ce74bc5a8d141f99a437a0c23e9d1379096a
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - autoconf
     - automake
+    - libtool
   host:
     - zlib
     - htslib
   run:
-    - zlib
     - htslib
 
 about:
-  home: https://github.com/smithlabcode/falco
+  home: 'https://github.com/smithlabcode/falco'
   license: GPL-3.0-only
+  license_family: GPL3
   license_file: LICENSE
   summary: |
     falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
-  doc_url: 'https://falco.readthedocs.io/'
+  doc_url: 'https://falco.readthedocs.io'
+  dev_url: 'https://github.com/smithlabcode/falco'
 
 test:
   commands:

diff --git a/recipes/fiji-simple_omero_client/meta.yaml b/recipes/fiji-simple_omero_client/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "fiji-simple_omero_client" %}
-{% set version = "5.18.0" %}
+{% set version = "5.19.0" %}
 
 package:
   name: {{ name | lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/GReD-Clermont/simple-omero-client/releases/download/{{ version }}/simple-omero-client-{{ version }}.jar
-  sha256: 0b70886437e9cf6c2ab1096d6e711c7319b45bac6784ab4aac5fb8ef98e64e61
+  sha256: 4d3e592b4d3bd2e9c692cab376d8a1b83ea29ba2a2d56d606ed5de09b5077734
 
 build:
   number: 0

diff --git a/recipes/galaxy-data/meta.yaml b/recipes/galaxy-data/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.1" %}
-{% set sha256 = "be4d1ba81589cc5e6d4fb38829c1770483cff6c380b7647aa80b7bc90737f573" %}
+{% set version = "24.1.2" %}
+{% set sha256 = "d75e5e9e954773c683cb54a655da0c9733f1c6b0f6e691fedb6a1edc6e4aede2" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:

diff --git a/recipes/galaxy-files/meta.yaml b/recipes/galaxy-files/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.1" %}
-{% set sha256 = "d3c23617eed928515fd492fd97588790b1c095fdd298b5f5584307f34846c4ca" %}
+{% set version = "24.1.2" %}
+{% set sha256 = "39f25b6f9a2f48625bf21fe0021e90768f598db1113867960420afc5988a4e70" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:

diff --git a/recipes/galaxy-objectstore/meta.yaml b/recipes/galaxy-objectstore/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.1.1" %}
-{% set sha256 = "0a38e7fedc5c9300507d441c17d745957e1c8a0c65d1b7efde62361bf024eff1" %}
+{% set version = "24.1.2" %}
+{% set sha256 = "1079e628fb89125792781e9a62711e8281f3cd34eff0cd5ce8ed452d6c06cb3e" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:

diff --git a/recipes/galaxy-schema/meta.yaml b/recipes/galaxy-schema/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "galaxy-schema" %}
-{% set version = "24.1.1" %}
-{% set sha256 = "622c65bf1f7fc0cfb5cf6ee844e819a7ceff2b929aca5894848761b3a7df84fa" %}
+{% set version = "24.1.2" %}
+{% set sha256 = "526d9c7e211da145f4169272a69b4a512304110da3dd9df61d0d305991db5309" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}
 
 package:

diff --git a/recipes/gempipe/meta.yaml b/recipes/gempipe/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.35.1" %}
+{% set version = "1.35.2" %}
 
 package:
     name: "gempipe"
@@ -7,7 +7,7 @@ package:
 
 source:
     url: https://github.com/lazzarigioele/gempipe/archive/v{{ version }}.tar.gz
-    sha256: 5fccf9b3d7e3eabca648df214b18b585976565db08bfc1845c63daf0f2812ad1
+    sha256: 4464468f342657119c7dba31c5809aa5cf2e2a536afd296c4d534b96c710de67
 
 
 build:

diff --git a/recipes/gfastats/meta.yaml b/recipes/gfastats/meta.yaml
@@ -10,7 +10,7 @@ source:
   git_tag: v{{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('gfastats', max_pin="x") }}
 
@@ -32,6 +32,9 @@ about:
   summary: The swiss army knife for genome assembly
 
 extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
   identifiers:
     - biotools:gfastats
     - usegalaxy-eu:gfastats

diff --git a/recipes/graphbin2/meta.yaml b/recipes/graphbin2/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "GraphBin2" %}
-{% set version = "1.3.2" %}
+{% set version = "1.3.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/metagentools/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 5cb611d539ac2608cf262ea5db39e4d81bc7c9c1a53ea2f5a47fb5d8abcb848a
+  sha256: 03ab89dbb6d26c9b414ff808598c295cf22fd3af22816a5c9fada94104a79686
 
 build:
   number: 0

diff --git a/recipes/hiphase/meta.yaml b/recipes/hiphase/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "hiphase" %}
-{% set version = "1.4.4" %}
-{% set hiphase_sha256 = "3fdff37542c0447e936525684a7e431430994ee810d60a43f319ae260a9161b0" %}
+{% set version = "1.4.5" %}
+{% set hiphase_sha256 = "144ed18b56873856073d27bb7daea757ab5cfe857685c033a64e331075107a04" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "IsoQuant" %}
-{% set version = "3.6.0" %}
-{% set sha256 = "510d12cb1f1edf7dbe4ba433681d2f5c3c1c15bc70711a24758884a08ef2d68b" %}
+{% set version = "3.6.1" %}
+{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %}
 
 package:
   name: {{ name | lower }}

diff --git a/recipes/metabolabpy/meta.yaml b/recipes/metabolabpy/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "metabolabpy" %}
-{% set version = "0.9.47" %}
-{% set sha256 = "9598c8df848403b31f98c926e053788ce9aed8d3e69749331fcb8393d460416c" %}
+{% set version = "0.9.48" %}
+{% set sha256 = "c606de4e2b6c469386910831a0ddf307ccc2658577c6b1507d89652edc399b6c" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/metacoag/meta.yaml b/recipes/metacoag/meta.yaml
@@ -1,17 +1,16 @@
 {% set name = "MetaCoAG" %}
-{% set version = "1.2.1" %}
+{% set version = "1.2.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/metagentools/{{ name }}/archive/v{{ version }}.tar.gz"
-  sha256: 5962a92e49842f55db50b7a7bede8dc33b9508a08d395a796b3f4fa78fed70b9
+  sha256: 1a8d91cb02fdad9ba15c636eeaf167e34f118bc4d12f57366e107ebf160781c7
 
 build:
   number: 0
-  noarch: python
   entry_points:
     - metacoag = metacoag.cli:main
     - combine_cov = metacoag.metacoag_utils.support.combine_cov:main
@@ -56,6 +55,8 @@ about:
   dev_url: "https://github.com/metagentools/MetaCoAG"
 
 extra:
+  skip-lints:
+    - should_be_noarch_generic
   recipe-maintainers:
     - Vini2
   identifiers:

diff --git a/recipes/phyloacc/build.sh b/recipes/phyloacc/build.sh
@@ -1,11 +1,13 @@
 #!/bin/bash
 
+set -xe
+
 mkdir -p ${PREFIX}/bin
 mkdir -p ${SP_DIR}
 
-make install CXX=${CXX}
+make -j ${CPU_COUNT} install CXX=${CXX}
 
 cp src/PhyloAcc-interface/phyloacc.py ${PREFIX}/bin/
 ln -s ${PREFIX}/bin/phyloacc.py ${PREFIX}/bin/phyloacc
 cp src/PhyloAcc-interface/phyloacc_post.py ${PREFIX}/bin/
-cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/
+cp -R src/PhyloAcc-interface/phyloacc_lib ${SP_DIR}/
diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 2
   skip: True  # [py < 38]
   run_exports:
     - {{ pin_subpackage('phyloacc', max_pin="x") }}
@@ -35,7 +35,7 @@ requirements:
     - matplotlib-base >=3.5
     - biopython >=1.79
     - numpy >=1.22
-    - snakemake-minimal >=7.3
+    - snakemake-minimal >=7.3,<8.0
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
 
@@ -56,5 +56,7 @@ about:
   dev_url: https://github.com/phyloacc/PhyloAcc
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - gwct