rmblast: add arm64/aarch64 builds (#52589)

* rmblast: add arm64/aarch64 builds * clean up recipe * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Try with double quotes for CONFIG_ARGS * Remove double quotes around ${CONFIG_ARGS} * s/ReleaseMT/Release/ --------- Co-authored-by: Martin Grigorov <[email protected]>
bioconda · Dec 5, 2024 · c7cd165 · c7cd165
1 parent 1d88d54
commit c7cd165
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Showing 2 changed files with 36 additions and 24 deletions.
diff --git a/recipes/rmblast/build.sh b/recipes/rmblast/build.sh
@@ -21,10 +21,10 @@ if [ `uname` == Darwin ]; then
     # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk for -D_LIBCPP_DISABLE_AVAILABILITY
     export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
 else
-    export CPP_FOR_BUILD=${CPP}
+    export CPP_FOR_BUILD="${CPP}"
 fi
 
-export LIB_INSTALL_DIR="${PREFIX}/lib/ncbi-blast+"
+export LIB_INSTALL_DIR="${PREFIX}/lib64/ncbi-blast+"
 
 # with/without options:
 #
@@ -53,55 +53,63 @@ export LIB_INSTALL_DIR="${PREFIX}/lib/ncbi-blast+"
 # Fixes building on Linux
 export AR="${AR} rcs"
 
-if [ `uname` == Linux ]; then
-  export CONFIG_ARGS="--with-openmp --with-hard-runpath --with-runpath=${LIB_INSTALL_DIR}"
+# Source path
+BLAST_SRC_DIR="$SRC_DIR/c++"
+# Work directory
+RESULT_PATH="$BLAST_SRC_DIR/Release"
+
+if [[ `uname` == "Linux" ]]; then
+	export CONFIG_ARGS="--with-runpath=\"${LIB_INSTALL_DIR}\" --with-openmp --with-hard-runpath --with-dll --without-zstd"
+	if [[ "$(uname -m)" == "x86_64" ]]; then
+            export CONFIG_ARGS="${CONFIG_ARGS} --with-64"
+	fi
 else
-  export CONFIG_ARGS="--without-openmp"
+	export CONFIG_ARGS='--without-openmp --without-dll --without-gcrypt'
 fi
 
 # not building with boost as it's only used for unit tests
 ./configure \
     CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" \
-    --prefix=${PREFIX} \
-    --with-64 \
+    --prefix="${PREFIX}" \
     --with-mt \
-    --without-dll \
+    --with-build-root="${RESULT_PATH}" \
+    --with-bin-release \
     --with-flat-makefile \
+    --without-autodep \
+    --without-makefile-auto-update \
     --without-caution \
     --without-boost \
     --without-lzo \
-    --without-zstd \
     --without-debug \
     --with-experimental=Int8GI \
-    --without-openssl \
     --with-strip \
-    --without-vdb \
-    --with-z=${PREFIX} \
-    --with-bz2=${PREFIX} \
+    --with-vdb="${PREFIX}" \
+    --with-z="${PREFIX}" \
+    --with-bz2="${PREFIX}" \
+    --with-sqlite3="${PREFIX}" \
     --without-krb5 \
     --without-gnutls \
     --without-sse42 \
-    --without-gcrypt \
     --without-pcre \
     ${CONFIG_ARGS}
 
 projects="algo/blast/ app/ objmgr/ objtools/align_format/ objtools/blast/"
-cd ReleaseMT
+cd Release
 
 # The "datatool" binary needs the libs at build time, create
 # link from final install path to lib build dir:
-ln -s ${SRC_DIR}/c++/ReleaseMT/lib ${LIB_INSTALL_DIR}
+ln -s ${SRC_DIR}/c++/Release/lib ${LIB_INSTALL_DIR}
 
 cd build
-make -j1 -f Makefile.flat all_projects="${projects}"
+make -j"${CPU_COUNT}" -f Makefile.flat all_projects="${projects}"
 
 # remove temporary link
 rm ${LIB_INSTALL_DIR}
 
 mkdir -p ${PREFIX}/bin ${LIB_INSTALL_DIR}
-chmod +x ${SRC_DIR}/c++/ReleaseMT/bin/*
-cp ${SRC_DIR}/c++/ReleaseMT/bin/* ${PREFIX}/bin/
-cp ${SRC_DIR}/c++/ReleaseMT/lib/* ${LIB_INSTALL_DIR}
+chmod +x ${SRC_DIR}/c++/Release/bin/*
+cp ${SRC_DIR}/c++/Release/bin/* ${PREFIX}/bin/
+cp ${SRC_DIR}/c++/Release/lib/* ${LIB_INSTALL_DIR}
 
 sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${PREFIX}/bin/update_blastdb.pl
 # Patches to enable this script to work better in bioconda

diff --git a/recipes/rmblast/meta.yaml b/recipes/rmblast/meta.yaml
@@ -18,7 +18,7 @@ source:
     - phonehome.patch
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('rmblast', max_pin="x") }}
 
@@ -33,10 +33,11 @@ requirements:
     - pcre
     - curl
     - time
+    - ncbi-vdb
+    - sqlite =3
   run:
-    - zlib
-    - bzip2
     - entrez-direct
+    - ncbi-vdb
     - perl
     - perl-list-moreutils
     - perl-archive-tar
@@ -73,12 +74,15 @@ test:
     - update_blastdb.pl --help
 
 about:
-  home: https://www.repeatmasker.org/rmblast/
+  home: https://www.repeatmasker.org/rmblast
   license: OSL-2.1
   summary: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite.
+  doc_url: https://www.repeatmasker.org/rmblast
 
 extra:
   identifiers:
     - biotools:rmblast
   recipe-maintainers:
     - mencian
+  additional-platforms:
+    - linux-aarch64