Fix MashMap v3.1.3 build. (#52373)

* Update mashmap build # to force rebuild * Update build.sh Disable OSX specific flags * Try without deployment target * Restore conda_build_config.yaml * Separate osx targets for arm vs x86 * Add OSX target to cmake cmd directly * Try to force macos SDK * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * Update build.sh * Update meta.yaml * Update conda_build_config.yaml * Update build.sh * Update conda_build_config.yaml * Update build.sh * Update build.sh --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
bioconda · Dec 4, 2024 · 31cae24 · 31cae24
1 parent 02bd1dd
commit 31cae24
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Showing 3 changed files with 33 additions and 18 deletions.
diff --git a/recipes/mashmap/build.sh b/recipes/mashmap/build.sh
@@ -2,15 +2,23 @@
 
 set -xe
 
-export CFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
+export CFLAGS="${CFLAGS} -I$PREFIX/include"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L$PREFIX/lib"
 export LD_LIBRARY_PATH="${PREFIX}/lib"
-export CPATH=${PREFIX}/include
+export CPATH="${PREFIX}/include"
 
-if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
-  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+if [[ `uname` == "Darwin" ]]; then
+  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY -D_LIBCPP_HAS_NO_LIBRARY_ALIGNED_ALLOCATION=1 -Wno-deprecated-builtins -Wno-vla-cxx-extension"
+  export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+  export CONFIG_ARGS=""
 fi  
 
-cmake -H. -B${PREFIX} -DCMAKE_BUILD_TYPE=Release -DCMAKE_VERBOSE_MAKEFILE=1 -DOPTIMIZE_FOR_NATIVE=0 -DUSE_HTSLIB=1 -DCMAKE_CXX_FLAGS="${CXXFLAGS}"
-cmake --build ${PREFIX} -j ${CPU_COUNT}
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+  -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+  -DCMAKE_VERBOSE_MAKEFILE=1 -DOPTIMIZE_FOR_NATIVE=0 \
+  -DUSE_HTSLIB=1 -DCMAKE_CXX_COMPILER="${CXX}" \
+  -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+  "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/mashmap/conda_build_config.yaml b/recipes/mashmap/conda_build_config.yaml
@@ -1,2 +1,3 @@
-MACOSX_DEPLOYMENT_TARGET:
-  - 10.15
+MACOSX_DEPLOYMENT_TARGET:     # [osx]
+  - 11.0                      # [osx and arm64]
+  - 10.15                     # [osx and x86_64]
diff --git a/recipes/mashmap/meta.yaml b/recipes/mashmap/meta.yaml
@@ -10,9 +10,9 @@ source:
   sha256: 7719dd6b3c25e650e16218252eaae7dbf424a10890d717ec3ad0920b102fd05a
 
 build:
-  number: 1
+  number: 2
   run_exports:
-    - {{ pin_subpackage("mashmap", max_pin="x.x") }}
+    - {{ pin_subpackage("mashmap", max_pin="x") }}
 
 # Refer to INSTALL.txt for details.
 requirements:
@@ -22,18 +22,16 @@ requirements:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
   host:
-    - perl =5.26
+    - perl
     - zlib
     - gsl
     - htslib
     - openblas
-    #- mkl  # [osx]
   run:
-    - zlib
     - gsl
     - htslib
     - openblas
-    #- mkl  # [osx]
+
 test:
   commands:
     - mashmap -h 2>&1 | grep 'reference_files'
@@ -42,12 +40,20 @@ about:
   home: "{{ github }}"
   dev_url: "{{ github }}"
   license: Custom
-  license_file: LICENSE.txt
-  summary: A fast approximate aligner for long DNA sequences.
+  license_file: "LICENSE.txt"
+  summary: "A fast approximate aligner for long DNA sequences."
+  doc_url: "https://github.com/marbl/MashMap/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   recipe-maintainers:
     - bkille
     - mjsteinbaugh
+  identifiers:
+    - biotools:mashmap
+    - usegalaxy-eu:mashmap
+    - doi:10.1101/2023.05.16.540882
+    - doi:10.1093/bioinformatics/bty597
+    - doi:10.1007/978-3-319-56970-3_5