Merge remote-tracking branch 'origin/saccharis' into saccharis

bioconda · Oct 26, 2024 · 32f9522 · 32f9522
2 parents a1c2b90 + a8cf104
commit 32f9522
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -772,9 +772,6 @@ recipes/perl-gd
 # sha mismatch when downloading source
 recipes/fmlrc2
 
-# tries to download zlib itself, which fails
-recipes/d4binding
-
 # no matching package named `quickersort` found
 recipes/mudskipper
 

diff --git a/recipes/abismal/build.sh b/recipes/abismal/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
-./configure --prefix=$PREFIX
-make CXXFLAGS="-O3 -D_LIBCPP_DISABLE_AVAILABILITY"
+
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
+./configure --prefix="$PREFIX"
+
+make CXXFLAGS="${CXXFLAGS} -O3 -D_LIBCPP_DISABLE_AVAILABILITY"
 make install
diff --git a/recipes/abismal/meta.yaml b/recipes/abismal/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.2.3" %}
+{% set version = "3.2.4" %}
 
 package:
   name: abismal
@@ -10,32 +10,36 @@ build:
     # abismal is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('abismal', max_pin="x.x") }}
 
-
 source:
   url: https://github.com/smithlabcode/abismal/releases/download/v{{ version }}/abismal-{{ version }}.tar.gz
-  sha256: 0698ca408feb7e2650468e66dfdd4615e9405f64cd5496272fe2226cefd21322
+  sha256: 822e5efe322f989c561a1fb728bd6f57f49d94033620eb1bc5046f22a8492544
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - autoconf
     - automake
-    - llvm-openmp  # [osx]
-    - libgomp      # [linux]
+    - libtool
   host:
     - zlib
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
   run:
     - htslib
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
 
 about:
-  home: https://github.com/smithlabcode/abismal
-  license: GPL-3.0-only
+  home: "https://github.com/smithlabcode/abismal"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
   summary: |
-    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads
-  doc_url: 'https://github.com/smithlabcode/abismal/blob/master/docs/MANUAL.md'
+    abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads.
+  doc_url: 'https://github.com/smithlabcode/abismal/blob/v{{ version }}/docs/MANUAL.md'
+  dev_url: "https://github.com/smithlabcode/abismal"
 
 test:
   commands:
@@ -45,3 +49,6 @@ extra:
   recipe-maintainers:
     - andrewdavidsmith
     - guilhermesena1
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/abyss/build.sh b/recipes/abyss/build.sh
@@ -1,5 +1,8 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 if [[ "$(uname)" == Darwin ]]; then
     # Fix for install_name_tool error:
     #   error: install_name_tool: changing install names or rpaths can't be
@@ -9,13 +12,14 @@ if [[ "$(uname)" == Darwin ]]; then
     export LDFLAGS="$LDFLAGS -headerpad_max_install_names"
 fi
 
-./configure \
-    --prefix="$PREFIX" \
-    --with-boost="$PREFIX" \
-    --with-mpi="$PREFIX" \
-    --with-sparsehash="$PREFIX" \
-    --without-sqlite || cat config.log
-make AM_CXXFLAGS=-Wall
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include" \
+	--with-boost="${PREFIX}" \
+	--with-mpi="${PREFIX}" \
+	--with-sparsehash="${PREFIX}" \
+	--without-sqlite || cat config.log
+make AM_CXXFLAGS="-Wall" -j"${CPU_COUNT}"
 make install
 
 $RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-pe" "$PREFIX/bin/abyss-pe.Makefile"

diff --git a/recipes/abyss/config.patch b/recipes/abyss/config.patch
diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "abyss" %}
-{% set version = "2.3.9" %}
+{% set version = "2.3.10" %}
 
 package:
   name: {{ name|lower }}
@@ -12,20 +12,22 @@ build:
 
 source:
   url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz
-  sha256: 55f0b27b67b4486dc6cbe132c0f4c228ee4f9e86c56292a7b50633df87e3212e
-  patches:
-    - config.patch
+  sha256: bbe42e00d1ebb53ec6afaad07779baaaee994aa5c65b9a38cf4ad2011bb93c65
 
 requirements:
   build:
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
   host:
     - boost-cpp
     - sparsehash
     - openmpi
     - btllib
   run:
+    - boost-cpp
     - openmpi
     - make
     - util-linux  # [linux]
@@ -38,12 +40,13 @@ test:
     - abyss-pe help | grep -q "Assemble reads into contigs and scaffolds"
 
 about:
-  home: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-  license: GPL-3.0-only
+  home: "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
-  dev_url: https://github.com/bcgsc/abyss
-  doc_url: https://github.com/bcgsc/abyss#readme
+  summary: "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler."
+  dev_url: "https://github.com/bcgsc/abyss"
+  doc_url: "https://github.com/bcgsc/abyss/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
@@ -54,5 +57,6 @@ extra:
     extended-base: true
   identifiers:
     - biotools:abyss
+    - usegalaxy-eu:abyss-pe
     - doi:10.1101/gr.214346.116
     - doi:10.1101/gr.089532.108
diff --git a/recipes/annembed/build.sh b/recipes/annembed/build.sh
@@ -5,4 +5,4 @@
 export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
-RUST_BACKTRACE=1 cargo install --features intel-mkl-static --verbose --path . --root $PREFIX
+RUST_BACKTRACE=1 cargo install --features intel-mkl-static,simdeez_f --verbose --path . --root $PREFIX
diff --git a/recipes/annembed/meta.yaml b/recipes/annembed/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.1.4" %}
+{% set version = "0.1.6" %}
 
 package:
   name: annembed
@@ -11,7 +11,7 @@ build:
   skip: True  # [osx]
 source:
   url: https://github.com/jianshu93/annembed/archive/v{{ version }}.tar.gz
-  sha256: 0f923798db3843aac0352eba5d2b169673ee087fce2cc37981bd19a1ecb878d0
+  sha256: f60dceb94df46ae2ccc7ed228988a67df254a28f02b9b545baf31ca6e85f7f8d
 
 requirements:
   build:
@@ -28,7 +28,7 @@ test:
 about:
   home: https://github.com/jianshu93/annembed
   license: MIT
-  summary: annembed is an ultra-fast and scalable non-linear dimension reduction algorithm (similar to UMAP or t-SNE) for large-scale biological data
+  summary: annembed is an ultra-fast and scalable non-linear dimension reduction/embedding algorithm (similar to UMAP or t-SNE) for large-scale biological data
 
 extra:
   maintainers:

diff --git a/recipes/assembly_finder/meta.yaml b/recipes/assembly_finder/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "assembly_finder" %}
-{% set version = "0.7.7" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/metagenlab/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0c6542253464b8ba406aeddc630f5625db74a5e1e07911534be3add0500a1f02
+  sha256: 8708d9185dccce21808777c79dad1c2b019ca1f416035c2e5e16b0c32928566e
 
 build:
-  number: 1
+  number: 0
   noarch: python
   entry_points:
     - assembly_finder=assembly_finder.__main__:main

diff --git a/recipes/augustus/build.sh b/recipes/augustus/build.sh
@@ -2,34 +2,39 @@
 
 set -x -e
 
-#export CXXFLAGS="${CXXFLAGS} -std=c++11 -stdlib=libstdc++ -stdlib=libc++ -DUSE_BOOST"
-export CXXFLAGS="${CXXFLAGS} -std=c++11  -DUSE_BOOST -I${PREFIX}/include"
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -std=c++14 -DUSE_BOOST -I${PREFIX}/include"
 
 mkdir -p ${PREFIX}/bin
 mkdir -p ${PREFIX}/scripts
 mkdir -p ${PREFIX}/config
 
 ## Make the software
-
-if [ "$(uname)" = Darwin ] ; then
-    # SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
-    sqlite=
+if [[ "$(uname)" = Darwin ]]; then
+	# SQLITE disabled due to compile issue, see: https://svn.boost.org/trac10/ticket/13501
+	sqlite=
 else
-    sqlite='SQLITE=true'
+	sqlite='SQLITE=true'
 fi
-make \
-    CC="${CC}" \
-    CXX="${CXX}" \
-    INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
-    LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
-    INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
-    LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
-    INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
-    LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
-    COMPGENPRED=true \
-    MYSQL=false \
-    $sqlite
 
+make \
+	CC="${CC}" \
+	CXX="${CXX}" \
+	INCLUDE_PATH_BAMTOOLS="-I${PREFIX}/include/bamtools" \
+	LIBRARY_PATH_BAMTOOLS="-L${PREFIX}/lib" \
+	INCLUDE_PATH_LPSOLVE="-I${PREFIX}/include/lpsolve" \
+	LIBRARY_PATH_LPSOLVE="-L${PREFIX}/lib" \
+	INCLUDE_PATH_HTSLIB="-I${PREFIX}/include/htslib" \
+	LIBRARY_PATH_HTSLIB="-L${PREFIX}/lib" \
+	COMPGENPRED=true \
+	MYSQL=false \
+	"${sqlite}" -j"${CPU_COUNT}"
+
+# Fix perl shebang
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SRC_DIR}/scripts/*.pl
+rm -rf ${SRC_DIR}/scripts/*.bak
 
 ## Build Perl
 
@@ -39,7 +44,7 @@ cd perl-build
 # affects tests for Augustus 3.3:
 # https://github.com/Gaius-Augustus/Augustus/commit/7ca3ab
 #sed -i'' -e '1s/perl -w/perl/' *.pl
-cp ${RECIPE_DIR}/Build.PL ./
+cp -f ${RECIPE_DIR}/Build.PL ./
 perl ./Build.PL
 perl ./Build manifest
 perl ./Build install --installdirs site
@@ -49,11 +54,11 @@ cd ..
 
 ## End build perl
 
+chmod 0755 bin/augustus
 mv bin/* $PREFIX/bin/
 mv scripts/* $PREFIX/bin/
 mv config/* $PREFIX/config/
 
-
 ## Set AUGUSTUS variables on env activation
 
 mkdir -p ${PREFIX}/etc/conda/activate.d ${PREFIX}/etc/conda/deactivate.d

diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml
@@ -1,28 +1,31 @@
+{% set name = "augustus" %}
 {% set version = "3.5.0" %}
 {% set sha256 = "5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686" %}
 
 package:
-  name: augustus
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/Gaius-Augustus/Augustus/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
+    - patches/0001-Makefile.patch
     - patches/homGeneMapping.src.makefile.patch
     - patches/utrrnaseq.patch
 
 build:
-  number: 4
+  number: 5
+  run_exports:
+    - {{ pin_subpackage('augustus', max_pin="x") }}
 
 requirements:
   build:
     - make
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host:
     - zlib
-    - samtools ==0.1.19
+    - samtools
     - bamtools
     - htslib
     - gsl
@@ -35,7 +38,6 @@ requirements:
     - perl
     - perl-module-build
   run:
-    - zlib
     - boost-cpp
     - gsl
     - lp_solve
@@ -152,19 +154,22 @@ test:
     - fix_in_frame_stop_codon_genes.py --help | grep -Fq 'fix_in_frame_stop_codon_genes.py'
 
 about:
-  home: http://bioinf.uni-greifswald.de/augustus/
-  license: Artistic Licence
+  home: "https://bioinf.uni-greifswald.de/augustus"
+  license: "Artistic Licence"
   license_family: Other
   license_file: "src/LICENSE.TXT"
   summary: 'AUGUSTUS is a gene prediction program for eukaryotes written by Mario
     Stanke and Oliver Keller. It can be used as an ab initio program, which means
     it bases its prediction purely on the sequence. AUGUSTUS may also incorporate
     hints on the gene structure coming from extrinsic sources such as EST, MS/MS,
     protein alignments and synthenic genomic alignments.'
+  dev_url: "https://github.com/Gaius-Augustus/Augustus"
+  doc_url: "https://github.com/Gaius-Augustus/Augustus/blob/v{{ version }}/docs/RUNNING-AUGUSTUS.md"
 
 extra:
   identifiers:
     - biotools:augustus
     - doi:10.1093/bioinformatics/btr010
     - usegalaxy-eu:augustus
+    - usegalaxy-eu:augustus_training
   notes: "Builds with sqlite support are currently only available on Linux due to compile issues with macOS."