Merge remote-tracking branch 'origin/master' #736
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| name: gw | |
| on: | |
| push: | |
| pull_request: | |
| env: | |
| version: 1.1.2 | |
| jobs: | |
| mingw: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| sys: [ucrt64] # clang64, | |
| name: ${{ matrix.sys }} | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: ${{ matrix.sys }} | |
| update: true | |
| install: make | |
| pacboy: toolchain:p glfw:p skia:p htslib:p freeglut:p glew:p ncurses:p fontconfig:p dlfcn:p libpng:p | |
| - name: build | |
| run: | | |
| make | |
| - name: upload | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: mingw-${{ matrix.sys }} | |
| path: ${{ github.workspace }}/*.exe | |
| macos-package: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ macos-14 ] # macos-12, | |
| include: | |
| - os: macos-13 | |
| arch: intel | |
| - os: macos-14 | |
| arch: m1 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| brew install imagemagick graphicsmagick dylibbundler glfw fontconfig | |
| brew list | grep python@ | |
| which python | |
| python --version | |
| python -m venv py_venv | |
| source py_venv/bin/activate | |
| python -m pip install --upgrade pip | |
| python -m pip install packaging | |
| npm install --global create-dmg | |
| which python && python --version | |
| which python3 && python3 --version | |
| - name: Build and install htslib with libdeflate | |
| run: | | |
| wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2 | |
| tar -xvf htslib.tar.bz2 && mv htslib-* htslib && rm htslib.tar.bz2 | |
| git clone --depth 1 https://github.com/ebiggers/libdeflate.git | |
| cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build | |
| cp build/libdeflate.a ../htslib | |
| cp libdeflate.h ../htslib | |
| ls ../htslib | |
| cd ../htslib | |
| LDFLAGS="$LDFLAGS -L./" CPPFLAGS="$CPPFLAGS -I./" ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate | |
| make | |
| sudo make install | |
| - name: Make Prep | |
| run: | | |
| make prep | |
| - name: package | |
| run: | | |
| osacompile -o gw.app deps/gw_applescript_prog.txt | |
| cp deps/gw_droplet.icns gw.app/Contents/Resources/droplet.icns | |
| echo "BUILDING GW" | |
| brew_lib=$(brew --prefix)/lib | |
| brew_include=$(brew --prefix)/include | |
| brew_bin=$(brew --prefix)/bin | |
| LDFLAGS="${LDFLAGS} -L${brew_lib}" CPPFLAGS="${CPPFLAGS} -I${brew_include}" make | |
| mv gw ./gw.app/Contents/MacOS | |
| rm -rf include lib src Makefile | |
| PATH="$PATH:$brew_bin" dylibbundler -od -b -x ./gw.app/Contents/MacOS/gw -d ./gw.app/Contents/libs/ -p @executable_path/../libs/ | |
| echo "VALIDATION" | |
| otool -L gw.app/Contents/MacOS/gw | |
| echo "" | |
| echo "CODE SIGNING" | |
| ls -l | |
| sudo chown -R $(whoami) ./gw.app | |
| chmod -R a+rw ./gw.app | |
| sudo codesign --remove-signature ./gw.app | |
| sudo codesign --force --deep -s - gw.app -v | |
| sudo codesign --verify -vvvv gw.app | |
| sudo hdiutil detach /Volumes/gw || true | |
| export TMPDIR=$(mktemp -d) | |
| PATH="$PATH:$brew_bin" create-dmg 'gw.app' || true | |
| ls | |
| mv gw\ undefined.dmg gw_macos_${{ matrix.arch }}.dmg | |
| ls | |
| pwd | |
| - name: upload | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: gw_macos_${{ matrix.arch }} | |
| path: ./*.dmg | |
| deb-package: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt-get install dh-make build-essential debhelper dh-virtualenv | |
| sudo apt-get install debugedit devscripts fakeroot debootstrap pbuilder autotools-dev | |
| sudo apt install zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libncursesw5-dev libssl-dev | |
| sudo apt install libgl1-mesa-dev libfontconfig-dev libcurl4-openssl-dev libglfw3 libglfw3-dev | |
| - name: build | |
| run: | | |
| BUILD_DIR=$(pwd) | |
| mkdir -p usr/bin | |
| mkdir -p usr/lib/x86_64-linux-gnu | |
| mkdir -p usr/lib/gwhts | |
| mkdir -p usr/include/gwhts | |
| mkdir -p usr/share/icons | |
| mkdir -p usr/share/icons/hicolor/512x512/apps/ | |
| mkdir -p usr/share/applications | |
| sudo mkdir -p /usr/lib/gwhts | |
| sudo mkdir -p /usr/include/gwhts/htslib | |
| sudo cp /usr/lib/x86_64-linux-gnu/libglfw* usr/lib/x86_64-linux-gnu/. | |
| git clone --depth 1 https://github.com/ebiggers/libdeflate.git | |
| cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build | |
| sudo cp build/libdeflate.a /usr/local/lib && sudo cp libdeflate.h /usr/local/include | |
| echo "LIBDEFLATE BUILT" && pwd | |
| cd ${BUILD_DIR} | |
| wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2 | |
| tar -xvf htslib.tar.bz2 | |
| mv htslib-1.20 htslib && rm htslib.tar.bz2 && cd htslib | |
| sed -i 's/ -g -Wall/ -Wall/' Makefile # strip debug information | |
| ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate | |
| make -j3 | |
| echo "HTSLIB BUILT" && pwd | |
| cp -rf htslib ../include | |
| sudo cp libhts.* /usr/lib/gwhts | |
| sudo cp htslib/*.h /usr/include/gwhts/htslib | |
| cp libhts.* ${BUILD_DIR}/usr/lib/gwhts | |
| cd ${BUILD_DIR} | |
| sed -i '133 i \\t-mv gw usr/bin' Makefile | |
| sed -i 's@-L/usr/local/lib@-L/usr/local/lib -L/usr/lib/gwhts@g' Makefile | |
| make prep | |
| cp include/gw_icon.png usr/share/icons/ | |
| cp include/gw_icon.png usr/share/icons/hicolor/512x512/apps/ | |
| cp deps/gw.desktop usr/share/applications/ | |
| - name: package | |
| run: | | |
| dh_make --single --createorig --packagename gw_${version} --email clealk@cardiff.ac.uk --yes --native | |
| printf "usr/bin/gw\nusr/share/icons/gw_icon.png\nusr/share/applications/gw.desktop\nusr/lib/gwhts/\nusr/lib/x86_64-linux-gnu/libglfw.so.3\nusr/lib/x86_64-linux-gnu/libglfw.so.3.3" > debian/install | |
| export LDFLAGS="$LDFLAGS -L./lib/skia/out/Release-x64 -L/usr/local/lib -L/usr/lib -L./usr/lib/gwhts -Wl,-rpath,'$ORIGIN/../lib/gwhts'" | |
| sed -i '/^Section/c\Section: Bioinformatics' debian/control | |
| sed -i '/^Homepage/c\Homepage: https://github.com/kcleal/gw' debian/control | |
| sed -i '/^Description/c\Description: Genome browser and variant annotation' debian/control | |
| sed -i '/<insert long/d' debian/control | |
| printf "Conflicts: libglfw3 (<< 3.3)\nReplaces: libglfw3\n" >> debian/control | |
| # Override dh_shlibdeps to include /usr/lib/gwhts | |
| printf '#!/usr/bin/make -f\n%%:\n\tdh $@\n\nclean:\n\tdh_clean\n\noverride_dh_shlibdeps:\n\tdh_shlibdeps -l/usr/lib/gwhts\n' > debian/rules | |
| chmod +x debian/rules | |
| dpkg-buildpackage -us -uc | |
| - name: upload | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: debian-package | |
| path: /home/runner/work/gw/*.deb |