Rebuild bam-readcount recipe

bioconda · Nov 20, 2024 · 10c1b48 · 10c1b48
1 parent a4a8e4f
commit 10c1b48
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Showing 2 changed files with 17 additions and 19 deletions.
diff --git a/recipes/bam-readcount/build.sh b/recipes/bam-readcount/build.sh
@@ -1,10 +1,8 @@
 #!/bin/bash -ex
 
-wget https://github.com/boostorg/boost/releases/download/boost-1.85.0/boost-1.85.0-cmake.tar.gz
+wget https://github.com/boostorg/boost/releases/download/boost-1.86.0/boost-1.86.0-cmake.tar.gz
 
-mv boost-1.85.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz
-
-mkdir -p "${PREFIX}/bin"
+mv boost-1.86.0-cmake.tar.gz vendor/boost-1.55-bamrc.tar.gz
 
 # Needed for building utils dependency
 export INCLUDES="-I{PREFIX}/include"
@@ -14,26 +12,22 @@ export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
 
 if [[ `uname` == Darwin ]]; then
 	export LDFLAGS="${LDFLAGS} -Wl,-rpath,${PREFIX}/lib"
-	export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wdeprecated-non-prototype"
+	export CFLAGS="${CFLAGS} -Wno-unguarded-availability -Wno-deprecated-non-prototype"
 	export CMAKE_EXTRA="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
 else
 	export CMAKE_EXTRA=""
 fi
 
-mkdir -p build
-pushd build
-cmake -S .. -B . -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
 	-DCMAKE_BUILD_TYPE=Release \
 	-DCMAKE_CXX_COMPILER="${CXX}" \
 	-DCMAKE_C_COMPILER="${CC}" \
 	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
 	-DCMAKE_C_FLAGS="${CFLAGS}" \
 	-Wno-dev -Wno-deprecated --no-warn-unused-cli \
-	${CMAKE_EXTRA}
+	"${CMAKE_EXTRA}"
 
-make clean
-make CXX="${CXX} ${LDFLAGS}" CC="${CC}" CXXFLAGS="${CXXFLAGS}" CFLAGS="${CFLAGS}"
+cmake --build build -j "${CPU_COUNT}" -v
 
-chmod 755 bin/bam-readcount
-cp -f bin/bam-readcount "${PREFIX}/bin"
-popd
+install -d "$PREFIX/bin"
+install -v -m 0755 bin/bam-readcount "$PREFIX/bin"
diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml
@@ -6,11 +6,11 @@ package:
   version: {{ version }}
 
 source:
-  url: https://github.com/genome/{{ name }}/archive/v{{ version }}.tar.gz
-  sha256: 8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8
+  git_url: https://github.com/genome/bam-readcount.git
+  git_rev: v{{ version }}
 
 build:
-  number: 2
+  number: 3
   run_exports:
     - {{ pin_subpackage('bam-readcount', max_pin="x") }}
 
@@ -19,7 +19,7 @@ requirements:
     - make
     - cmake
     - {{ compiler('cxx') }}
-    - {{ compiler('c') }}
+    - libtool
   host:
     - zlib
     - pthread-stubs
@@ -39,11 +39,15 @@ about:
   license_file: LICENSE
   summary: "bam-readcount generates metrics at single nucleotide positions."
   dev_url: "https://github.com/genome/bam-readcount"
-  doc_url: "https://github.com/genome/bam-readcount/blob/master/README.md"
+  doc_url: "https://github.com/genome/bam-readcount/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   identifiers:
     - doi:10.21105/joss.03722
     - biotools:bam-readcount
+  skip-lints:
+    - uses_vcs_url
+    - missing_hash