Update sra-tools recipe (bioconda#50594)

* Update sra-tools recipe * Update sra-tools recipe
mencian · Sep 10, 2024 · 21244fe · 21244fe
1 parent 3064eb8
commit 21244fe
Show file tree

Hide file tree

Showing 2 changed files with 27 additions and 21 deletions.
diff --git a/recipes/sra-tools/build.sh b/recipes/sra-tools/build.sh
@@ -4,12 +4,6 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 -DH5_USE_110_API -D_FILE_OFFSET_BITS=64 ${LDFLAGS}"
 export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
-echo "compiling sra-tools"
-if [[ ${OSTYPE} == "darwin"* ]]; then
-    export CFLAGS="${CFLAGS} -DTARGET_OS_OSX"
-    export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX"
-fi
-
 mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc  # prevent error on OSX
 
 
@@ -18,22 +12,32 @@ mkdir -p obj/ngs/ngs-java/javadoc/ngs-doc  # prevent error on OSX
 export SRA_BUILD_DIR=${SRC_DIR}/build_sratools
 mkdir -p ${SRA_BUILD_DIR}
 
+echo "Compiling sra-tools"
 if [[ "$(uname)" == "Darwin" ]]; then
-    export VDB_INC="${SRC_DIR}/ncbi-vdb/interfaces"
+	export VDB_INC="${SRC_DIR}/ncbi-vdb/interfaces"
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+	export CFLAGS="${CFLAGS} -DTARGET_OS_OSX"
+	export CXXFLAGS="${CXXFLAGS} -DTARGET_OS_OSX"
 else
-    export VDB_INC="${PREFIX}/include"
+	export VDB_INC="${PREFIX}/include"
+	export CONFIG_ARGS=""
 fi
 
 cmake -S sra-tools/ -B build_sratools/ \
-    -DVDB_BINDIR="${PREFIX}" \
-    -DVDB_LIBDIR="${PREFIX}/lib64" \
-    -DVDB_INCDIR="${VDB_INC}" \
-    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-    -DCMAKE_BUILD_TYPE=Release \
-    -DCMAKE_CXX_COMPILER="${CXX}" \
-    -DCMAKE_CXX_FLAGS="${CXXFLAGS}"
-
-cmake --build build_sratools/ --target install -j ${CPU_COUNT} -v
+	-DVDB_BINDIR="${PREFIX}" \
+	-DVDB_LIBDIR="${PREFIX}/lib" \
+	-DVDB_INCDIR="${VDB_INC}" \
+	-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release \
+	-DBUILD_SHARED_LIBS=ON \
+	-DCMAKE_INSTALL_LIBDIR="${PREFIX}/lib" \
+	-DCMAKE_C_COMPILER="${CC}" \
+	-DCMAKE_C_FLAGS="${CFLAGS}" \
+	-DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+
+cmake --build build_sratools/ --target install -j "${CPU_COUNT}" -v
 
 
 # Strip package version from binary names

diff --git a/recipes/sra-tools/meta.yaml b/recipes/sra-tools/meta.yaml
@@ -15,7 +15,7 @@ source:
   folder: ncbi-vdb  # [osx]
 
 build:
-  number: 0
+  number: 2
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
@@ -55,14 +55,16 @@ test:
 
 about:
   home: "https://github.com/ncbi/sra-tools"
-  license: Public Domain
+  license: "Public Domain"
   summary: "The SRA Toolkit and SDK from NCBI."
   description:  |
-    The SRA Toolkit and SDK from NCBI is a collection of tools and libraries
-    for using data in the INSDC Sequence Read Archives.
+    "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries
+    for using data in the INSDC Sequence Read Archives."
   dev_url: "https://github.com/ncbi/sra-tools"
   doc_url: "https://github.com/ncbi/sra-tools/wiki"
 
 extra:
   notes: 'After installation, you should run the configuration tool: ./vdb-config
     -i. This tool will setup your download/cache area for downloaded files and references.'
+  identifiers:
+    - biotools:sra-tools