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cuttlefish: add arm64 build #51956

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merged 6 commits into from
Nov 6, 2024
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cuttlefish: add arm64 build #51956

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bb84fd7
cuttlefish: add aarch64/arm64 builds
mencian Nov 6, 2024
8cb61a0
remove autoconf
mencian Nov 6, 2024
7aefeb9
add patch
mencian Nov 6, 2024
9553e4e
edit build.sh
mencian Nov 6, 2024
5b842be
Update build.sh
mencian Nov 6, 2024
e57fd98
Update build.sh
mencian Nov 6, 2024
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39 changes: 20 additions & 19 deletions recipes/cuttlefish/build.sh
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Original file line number Diff line number Diff line change
@@ -1,24 +1,25 @@
#!/bin/bash

mkdir build
cd build
export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include"
Comment on lines +3 to +6
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🛠️ Refactor suggestion

Optimize environment variable configuration

Several suggestions to improve the build configuration:

  1. INCLUDES and LIBPATH appear redundant as they're already covered by CXXFLAGS and LDFLAGS
  2. The -fcommon flag suggests potential symbol collision issues. Consider fixing the multiple symbol definitions instead
  3. Consider adding architecture-specific optimizations for ARM64 builds
-export INCLUDES="-I${PREFIX}/include"
-export LIBPATH="-L${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
-export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
+if [[ "${target_platform}" == "osx-arm64" ]]; then
+    export CXXFLAGS="${CXXFLAGS} -mcpu=apple-m1"
+fi
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"
if [[ "${target_platform}" == "osx-arm64" ]]; then
export CXXFLAGS="${CXXFLAGS} -mcpu=apple-m1"
fi


unamestr=`uname`

if [ "$unamestr" == 'Darwin' ];
then
export MACOSX_DEPLOYMENT_TARGET=10.15
export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY"
else
# It's dumb and absurd that the KMC build can't find the bzip2 header <bzlib.h>
export C_INCLUDE_PATH="$PREFIX/include"
export CPLUS_INCLUDE_PATH="$PREFIX/include"
if [[ `uname` == 'Darwin' ]]; then
export MACOSX_DEPLOYMENT_TARGET=10.11
export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
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⚠️ Potential issue

Review macOS deployment target for ARM64 compatibility

Setting MACOSX_DEPLOYMENT_TARGET=10.11 might be too old for ARM64 support, as Apple Silicon requires at least macOS 11.0 (Big Sur).

 if [[ `uname` == 'Darwin' ]]; then
-    export MACOSX_DEPLOYMENT_TARGET=10.11
+    if [[ "${target_platform}" == "osx-arm64" ]]; then
+        export MACOSX_DEPLOYMENT_TARGET=11.0
+    else
+        export MACOSX_DEPLOYMENT_TARGET=10.11
+    fi
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
if [[ `uname` == 'Darwin' ]]; then
export MACOSX_DEPLOYMENT_TARGET=10.11
export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
if [[ `uname` == 'Darwin' ]]; then
if [[ "${target_platform}" == "osx-arm64" ]]; then
export MACOSX_DEPLOYMENT_TARGET=11.0
else
export MACOSX_DEPLOYMENT_TARGET=10.11
fi
export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"

else
# It's dumb and absurd that the KMC build can't find the bzip2 header <bzlib.h>
export C_INCLUDE_PATH="$PREFIX/include"
export CPLUS_INCLUDE_PATH="$PREFIX/include"
export CONFIG_ARGS=""
fi

cmake \
-DINSTANCE_COUNT=64 \
-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
-DCONDA_BUILD=ON \
..
make install
cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
-DINSTANCE_COUNT=64 \
-DCMAKE_INSTALL_PREFIX="${PREFIX}" \
"${CONFIG_ARGS}"
cmake --build build/ --target install -j "${CPU_COUNT}" -v
104 changes: 0 additions & 104 deletions recipes/cuttlefish/build_failure.osx-64.yaml
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24 changes: 12 additions & 12 deletions recipes/cuttlefish/meta.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,28 +6,24 @@ package:
version: {{ version }}

build:
number: 2
number: 3
run_exports:
- {{ pin_subpackage('cuttlefish', max_pin="x") }}

source:
url: https://github.com/COMBINE-lab/cuttlefish/archive/refs/tags/v{{ version }}.tar.gz
sha256: d524aaeed5dd86ce256c5540661eda388cecbfad2ce4dde86e52539b2b1d6ed5

requirements:
build:
- autoconf
- cmake >=3.14.0
- make
- {{ compiler('cxx') }}
- {{ compiler('c') }}
- zlib
- bzip2
host:
- jemalloc >=5.1.0
- zlib
- bzip2
run:
- bzip2
- zlib

test:
commands:
Expand All @@ -36,17 +32,21 @@ test:
- cuttlefish version

about:
home: https://github.com/COMBINE-lab/cuttlefish
license: BSD-3-Clause
home: "https://github.com/COMBINE-lab/cuttlefish"
license: "BSD-3-Clause"
license_family: BSD
license_file: LICENSE
summary: Construction of the compacted de Bruijn graph efficiently
dev_url: https://github.com/COMBINE-lab/cuttlefish
doc_url: https://github.com/COMBINE-lab/cuttlefish#readme
summary: "Construction of the compacted de Bruijn graph efficiently."
dev_url: "https://github.com/COMBINE-lab/cuttlefish"
doc_url: "https://github.com/COMBINE-lab/cuttlefish/blob/v{{ version }}/README.md"

extra:
additional-platforms:
- osx-arm64
recipe-maintainers:
- jamshed
- rob-p
identifiers:
- doi:10.1093/bioinformatics/btab309
- doi:10.1186/s13059-022-02743-6
- biotools:cuttlefish