From 1da9c75d032389d9529f76b4f4d622fd3d6f844a Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Tue, 3 Dec 2024 14:55:16 +0200 Subject: [PATCH 1/4] quast: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov --- recipes/quast/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index bbe2024660d3b..7815e1b6d6632 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage("quast", max_pin="x.x") }} @@ -66,6 +66,8 @@ about: summary: Quality Assessment Tool for Genome Assemblies extra: + additional-platforms: + - linux-aarch64 container: # ascii fallback fails without locale extended-base: true From f04b9c9af708055818041d57be2c8bb0f176352a Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 5 Feb 2025 03:00:47 -0600 Subject: [PATCH 2/4] Update meta.yaml --- recipes/quast/meta.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index 7815e1b6d6632..4e4287416d1ab 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -8,7 +8,7 @@ package: build: number: 1 run_exports: - - {{ pin_subpackage("quast", max_pin="x.x") }} + - {{ pin_subpackage("quast", max_pin="x") }} source: url: @@ -30,6 +30,7 @@ requirements: - python - pip - setuptools + - cython - matplotlib-base - joblib - simplejson @@ -37,18 +38,18 @@ requirements: - zlib - glimmerHMM - circos - - minimap2 >=2.10 + - minimap2 run: - perl - python - matplotlib-base - - openjdk >=8 + - openjdk >=11.0.1 - joblib - simplejson - blast - glimmerHMM - circos - - minimap2 >=2.10 + - minimap2 - bedtools - bwa @@ -60,19 +61,22 @@ test: - metaquast --version about: - home: http://quast.sourceforge.net/ + home: "https://quast.sourceforge.net" license: Custom license_file: LICENSE.txt - summary: Quality Assessment Tool for Genome Assemblies + summary: "Quality Assessment Tool for Genome Assemblies." + dev_url: "https://github.com/ablab/quast" + doc_url: "https://quast.sourceforge.net/docs/manual.html" extra: additional-platforms: - linux-aarch64 container: # ascii fallback fails without locale - extended-base: true + extended-base: True notes: | - GeneMark gene prediction software is disabled due to licensing issues identifiers: - biotools:quast + - usegalaxy-eu:quast - doi:10.1093/bioinformatics/btt086 From 1fa2671701b78ab6118f056507657392472c4107 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 5 Feb 2025 03:05:32 -0600 Subject: [PATCH 3/4] Update build.sh --- recipes/quast/build.sh | 28 ++++++++++++---------------- 1 file changed, 12 insertions(+), 16 deletions(-) diff --git a/recipes/quast/build.sh b/recipes/quast/build.sh index 41b064b562fa8..d036e8556de70 100644 --- a/recipes/quast/build.sh +++ b/recipes/quast/build.sh @@ -3,7 +3,8 @@ export C_INCLUDE_PATH=$PREFIX/include export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" -export LD_LIBRARY_PATH="${PREFIX}/lib" +export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" BINARY_HOME=$PREFIX/bin QUAST_HOME=$PREFIX/opt/quast-$PKG_VERSION @@ -14,17 +15,12 @@ mkdir -p $QUAST_HOME rm -rf $SRC_DIR/quast_libs/site_packages/joblib* rm -rf $SRC_DIR/quast_libs/site_packages/simplejson -sed -i'.bak' 's/CC=/#CC=/' $SRC_DIR/quast_libs/bwa/Makefile -sed -i'.bak' 's/INCLUDES=/#INCLUDES=/' $SRC_DIR/quast_libs/bwa/Makefile -sed -i'.bak' 's/CFLAGS=/CFLAGS+= -fcommon/' $SRC_DIR/quast_libs/bwa/Makefile +sed -i.bak 's/CC=/#CC=/' $SRC_DIR/quast_libs/bwa/Makefile +sed -i.bak 's/INCLUDES=/#INCLUDES=/' $SRC_DIR/quast_libs/bwa/Makefile +sed -i.bak 's/CFLAGS=/CFLAGS+= -fcommon/' $SRC_DIR/quast_libs/bwa/Makefile -#pushd $SRC_DIR/quast_libs/bwa/ -#make -#mv bwa ${PREFIX}/bin -#popd - -sed -i'.bak' 's/export CXX\s/#export CXX/' $SRC_DIR/quast_libs/bedtools/Makefile -sed -i'.bak' 's/CXXFLAGS =/CXXFLAGS +=/' $SRC_DIR/quast_libs/bedtools/Makefile +sed -i.bak 's/export CXX\s/#export CXX/' $SRC_DIR/quast_libs/bedtools/Makefile +sed -i.bak 's/CXXFLAGS =/CXXFLAGS +=/' $SRC_DIR/quast_libs/bedtools/Makefile # Fails on OSX #pushd $SRC_DIR/quast_libs/bedtools/ @@ -32,7 +28,7 @@ sed -i'.bak' 's/CXXFLAGS =/CXXFLAGS +=/' $SRC_DIR/quast_libs/bedtools/Makefile #cp ./bin/* ${PREFIX}/bin #popd -$PYTHON -m pip install . --ignore-installed --no-deps -vv +$PYTHON -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv tail -n50 $SRC_DIR/quast_libs/*/make.* || true @@ -41,14 +37,14 @@ cp -R $SRC_DIR/icarus.py $QUAST_HOME/ lib_path=`python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())"` -ln -s $lib_path/quast_libs $QUAST_HOME/quast_libs +ln -sf $lib_path/quast_libs $QUAST_HOME/quast_libs #Linking to binfolder chmod +x $QUAST_HOME/quast.py -ln -s "$QUAST_HOME/quast.py" "$BINARY_HOME/quast" +ln -sf "$QUAST_HOME/quast.py" "$BINARY_HOME/quast" chmod +x $QUAST_HOME/metaquast.py -ln -s "$QUAST_HOME/metaquast.py" "$BINARY_HOME/metaquast" +ln -sf "$QUAST_HOME/metaquast.py" "$BINARY_HOME/metaquast" -cp $RECIPE_DIR/quast-download-* $PREFIX/bin +cp -rf $RECIPE_DIR/quast-download-* $PREFIX/bin chmod +x $PREFIX/bin/quast-download-* From 30ffd7ba5c003937661dc8ccd9fe8159a7a50b6f Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Wed, 5 Feb 2025 03:09:38 -0600 Subject: [PATCH 4/4] Update meta.yaml --- recipes/quast/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index 4e4287416d1ab..43282035e6f83 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 run_exports: - {{ pin_subpackage("quast", max_pin="x") }}