Update percolator to version 3.6.5 (bioconda#47414)

* Percolator version 3.6.5 * Add run_exports * Remove from blacklist, fingers crossed * Maybe it works if I add libboost-devel? * Boost 1.71 has static libraries which percolator needs * Whoops, typo in package version spec * clean up recipe * edit build.sh * revert to skipping osx --------- Co-authored-by: mencian <[email protected]> Co-authored-by: Joshua Zhuang <[email protected]>
mencian · Apr 25, 2024 · 830f3ea · 830f3ea
1 parent dd9955e
commit 830f3ea
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -231,7 +231,6 @@ recipes/bmtool
 recipes/sibelia
 recipes/var-agg
 recipes/wham
-recipes/percolator
 
 # Segfaults in bulk on Linux 24.3.2021
 recipes/dbgraph

diff --git a/recipes/percolator/build.sh b/recipes/percolator/build.sh
@@ -1,20 +1,30 @@
 #!/bin/bash
 
-mkdir percobuild && cd percobuild
-cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$PREFIX -DXML_SUPPORT=ON -DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_FLAGS="-std=c++14" $SRC_DIR
-make && make install
-cd ..
+export INCLUDES="-I{PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+cmake -S . -B percobuild \
+	-DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="$PREFIX" -DXML_SUPPORT=ON \
+	-DCMAKE_PREFIX_PATH="$PREFIX;$PREFIX/lib" -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="-std=c++14 -O3 -I{PREFIX}/include"
+cmake --build percobuild/ --target install -j ${CPU_COUNT} -v
 
 # First make sure we dont get problems with truncated PREFIX due to null terminators:
 # see percolator/percolator#251 and conda/conda-build#1674
-sed -i '54s/WRITABLE_DIR/std::string(WRITABLE_DIR).c_str()/' $SRC_DIR/src/Globals.cpp
-mkdir converterbuild && cd converterbuild 
-cmake -DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT=$PREFIX -DBOOST_LIBRARYDIR=$PREFIX/lib -DSERIALIZE="Boost" -DCMAKE_CXX_FLAGS="-std=c++11" -DCMAKE_PREFIX_PATH="$PREFIX" $SRC_DIR/src/converters
-make install
-cd ..
+sed -i.bak '54s/WRITABLE_DIR/std::string(WRITABLE_DIR).c_str()/' $SRC_DIR/src/Globals.cpp
+
+cmake -S ${SRC_DIR}/src/converters -B converterbuild \
+	-DTARGET_ARCH=x86_64 -DCMAKE_BUILD_TYPE=Release \
+	-DCMAKE_INSTALL_PREFIX="$PREFIX" -DBOOST_ROOT="$PREFIX" \
+	-DBOOST_LIBRARYDIR="$PREFIX/lib" -DSERIALIZE="Boost" \
+	-DCMAKE_CXX_FLAGS="-std=c++11 -O3 -I{PREFIX}/include" \
+	-DCMAKE_PREFIX_PATH="$PREFIX" -DCMAKE_CXX_COMPILER="${CXX}"
+cmake --build converterbuild/ --target install -j ${CPU_COUNT} -v
 
-mkdir $PREFIX/testdata
-cp $SRC_DIR/src/converters/data/converters/sqt2pin/target.sqt $PREFIX/testdata/target.sqt
-cp $SRC_DIR/src/converters/data/converters/msgf2pin/target.mzid $PREFIX/testdata/target.mzid
-cp $SRC_DIR/src/converters/data/converters/tandem2pin/target.t.xml $PREFIX/testdata/target.t.xml
-cp $SRC_DIR/data/percolator/tab/percolatorTab $PREFIX/testdata/percolatorTab
+mkdir -p $PREFIX/testdata
+cp -f $SRC_DIR/src/converters/data/converters/sqt2pin/target.sqt $PREFIX/testdata/target.sqt
+cp -f $SRC_DIR/src/converters/data/converters/msgf2pin/target.mzid $PREFIX/testdata/target.mzid
+cp -f $SRC_DIR/src/converters/data/converters/tandem2pin/target.t.xml $PREFIX/testdata/target.t.xml
+cp -f $SRC_DIR/data/percolator/tab/percolatorTab $PREFIX/testdata/percolatorTab
diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml
@@ -1,25 +1,27 @@
 {% set name = "percolator" %}
-{% set version = "3.5" %}
+{% set version = "3.6.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/percolator/percolator/archive/rel-3-05.tar.gz
-  sha256: 5b746bdc0119a40f96bc090e02e27670f91eeb341736911750b170da7e5c06bb
+  url: https://github.com/percolator/percolator/archive/refs/tags/rel-3-06-05.tar.gz
+  sha256: e386998046f59c34be01b1b0347709751d92f3a98e9a0079f8e7c5af5e2dcc8f
 
 build:
-  number: 2
-  skip: True # [osx]
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('percolator', max_pin="x") }}
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - cmake
   host:
-    - boost
+    - boost-cpp 1.71  # last version to have static libs
     - sqlite
     - bzip2
     - xerces-c
@@ -38,13 +40,17 @@ test:
 
 about:
   home: https://github.com/percolator/percolator
-  license: Apache 2.0
+  license: Apache-2.0
+  license_family: APACHE
   license_file: license.txt
   summary: Semi-supervised learning for peptide identification from shotgun proteomics datasets
+  dev_url: https://github.com/percolator/percolator
+  doc_url: http://percolator.ms/
 
 extra:
   container:
-    extended-base: true  # Add UTF-8 for percolator converters
+    extended-base: True  # Add UTF-8 for percolator converters
   identifiers:
     - biotools:Percolator
     - doi:10.1007/s13361-016-1460-7
+    - usegalaxy-eu:percolator