quast: add linux-aarch64 build (#52546)

* quast: add linux-aarch64 build

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

* Update meta.yaml

* Update build.sh

* Update meta.yaml

* Try with Python 3.12+

* Use Python 3.12+ only for aarch64

* Python 3.12+ for all. linux-64 tests failed

---------

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>

Author: martin-g

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
@@ -14,25 +15,20 @@ 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/
 #make
 #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-*

recipes/quast/meta.yaml

@@ -6,9 +6,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
   run_exports:
-    - {{ pin_subpackage("quast", max_pin="x.x") }}
+    - {{ pin_subpackage("quast", max_pin="x") }}
 
 source:
   url:
@@ -27,28 +27,29 @@ requirements:
     - make
   host:
     - perl
-    - python
+    - python >=3.12
     - pip
     - setuptools
+    - cython
     - matplotlib-base
     - joblib
     - simplejson
     - blast
     - zlib
     - glimmerHMM
     - circos
-    - minimap2 >=2.10
+    - minimap2
   run:
     - perl
-    - python
+    - python >=3.12
     - matplotlib-base
-    - openjdk >=8
+    - openjdk >=11.0.1
     - joblib
     - simplejson
     - blast
     - glimmerHMM
     - circos
-    - minimap2 >=2.10
+    - minimap2
     - bedtools
     - bwa
 
@@ -60,17 +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