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stschiffstschiff
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updated gh-workflow
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‎.github/workflows/Dockerfile.centos‎

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FROM quay.io/condaforge/linux-anvil-cos7-x86_64
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RUN yum -y update
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RUN yum -y install zlib-devel wget ncurses-devel ncurses-compat-libs make gcc gcc-c++
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# Install GHC since stack's local install has issues
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RUN wget https://downloads.haskell.org/~ghc/9.4.7/ghc-9.4.7-x86_64-centos7-linux.tar.xz
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RUN tar xvf ghc-9.4.7-x86_64-centos7-linux.tar.xz
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RUN cd ghc-9.4.7-x86_64-unknown-linux; ./configure; make install
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# install stack
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RUN curl -sSL https://get.haskellstack.org/ | sh
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# add source directory
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ADD . source
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WORKDIR source
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# install
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# - as described in cryptonite README, cryptoniate requires disabling "use_target_attributes"
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# - for bitvec the "simd" flag added in v1.1.5.0 has to be deactivated - the gcc version here does not seem to support it
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RUN stack install --system-ghc --flag cryptonite:-use_target_attributes --flag bitvec:-simd

‎.github/workflows/release.yaml‎

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name: Release
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on:
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# Trigger the workflow on the new 'v*' tag created
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push:
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name: Release ${{ github.ref_name }}
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draft: true
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# build-on-centos:
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# runs-on: ubuntu-latest
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# steps:
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# - name: Checkout repo
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# uses: actions/checkout@v2
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# - name: Build Docker image
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# run: docker build -t linux -f Dockerfile.linux .
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# - name: Create container
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# run: docker create --name linuxcontainer linux
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# - name: Copy executable
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# run: |
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# for TOOL in genoStats pileupCaller vcf2eigenstrat; do
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# docker cp linuxcontainer:/root/.local/bin/$TOOL $TOOL-linux
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# done
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# - name: update-release
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# run: |
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# for TOOL in genoStats pileupCaller vcf2eigenstrat; do
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# bash .github/workflows/upload-github-release-asset.sh github_api_token=${{ secrets.GITHUB_TOKEN }} owner=stschiff repo=sequenceTools tag=$(basename $GITHUB_REF) filename=$TOOL-linux
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# done
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build:
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build_normal_artifacts:
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needs: [create_release]
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name: ${{ matrix.os }}/${{ github.ref_name }}
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name: ${{ matrix.os }}/${{ github.ref }}
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runs-on: ${{ matrix.os }}
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continue-on-error: true
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strategy:
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fail-fast: false
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matrix:
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os: [macos-latest,ubuntu-20.04,windows-latest]
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os: [ubuntu-20.04, macOS-13, macOS-14, windows-latest]
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2
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- name: Setup Haskell
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uses: haskell-actions/setup@v2
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with:
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ghc-version: "9.4.7"
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enable-stack: true
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stack-version: "latest"
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- name: Build
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run: stack install --system-ghc
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- name: Rename binaries (not windows)
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if: ${{ matrix.os != 'windows-latest' }}
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run: for TOOL in genoStats pileupCaller vcf2eigenstrat; do mv ~/.local/bin/$TOOL ~/.local/bin/$TOOL-$RUNNER_OS; done
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- name: Rename binaries (windows)
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if: ${{ matrix.os == 'windows-latest' }}
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# stack on windows installs into <Home>\AppData\Roaming\local\bin
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# the default shell on Windows is powershell, so we use that
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run: |
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foreach ($tool in "genoStats", "pileupCaller", "vcf2eigenstrat") { Rename-Item "$env:USERPROFILE\AppData\Roaming\local\bin\$tool.exe" "$tool-windows.exe" }
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- name: Upload Release Asset (not windows)
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uses: ncipollo/release-action@v1
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if: ${{ matrix.os != 'windows-latest' }}
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with:
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name: Release ${{ github.ref_name }}
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draft: true
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allowUpdates: true
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artifactErrorsFailBuild: true
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artifacts: "~/.local/bin/*"
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artifactContentType: application/octet-stream
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- name: Upload Release Asset (windows)
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uses: ncipollo/release-action@v1
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if: ${{ matrix.os == 'windows-latest' }}
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with:
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name: Release ${{ github.ref_name }}
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draft: true
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allowUpdates: true
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artifactErrorsFailBuild: true
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artifacts: '~/AppData/Roaming/local/bin/*.exe'
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artifactContentType: application/octet-stream
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set tag name
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uses: olegtarasov/get-tag@v2.1
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id: tagName
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with:
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tagRegex: "v(.*)"
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tagRegexGroup: 1
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- name: Install stack on macOS, where it is not present (https://github.com/freckle/stack-action/issues/80)
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if: ${{ runner.os == 'macOS' }}
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run: curl -sSL https://get.haskellstack.org/ | sh
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- name: Build executable
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uses: freckle/stack-action@v5
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id: stack
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with:
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test: false
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stack-build-arguments: --copy-bins --ghc-options="-O2"
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- name: Set binary path name
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id: binarypath
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run: |
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if [ "$RUNNER_OS" == "Windows" ]; then
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newEXE="pileupCaller-$RUNNER_OS.exe"
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elif [ "$RUNNER_OS" == "macOS" ]; then
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newEXE="pileupCaller-$RUNNER_OS-$RUNNER_ARCH"
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else
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newEXE="pileupCaller-$RUNNER_OS"
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fi
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currentEXE="${{ steps.stack.outputs.local-bin }}/pileupCaller"
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mv $currentEXE $newEXE
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echo "BINARY_PATH=$newEXE" >> $GITHUB_OUTPUT
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shell: bash
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- name: Compress binary
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if: ${{ runner.os != 'macOS' }} # upx is crashing for macOS Ventura or above!
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uses: svenstaro/upx-action@v2
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with:
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files: ${{ steps.binarypath.outputs.BINARY_PATH }}
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- name: Upload Release Asset
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id: upload-release-asset
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uses: ncipollo/release-action@v1
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with:
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name: Release ${{ github.ref_name }}
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draft: true
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allowUpdates: true
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artifactErrorsFailBuild: true
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artifacts: ${{ steps.binarypath.outputs.BINARY_PATH }}
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artifactContentType: application/octet-stream
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build_centos_artifact:
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needs: [create_release]
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Build Docker image
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run: docker build -t linux -f .github/workflows/Dockerfile.centos .
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- name: Create container
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run: docker create --name linuxcontainer linux
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- name: Copy executable
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run: docker cp linuxcontainer:/root/.local/bin/pileupCaller pileupCaller-conda-linux
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- name: Upload Release Asset
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id: upload-release-asset
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uses: ncipollo/release-action@v1
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with:
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name: Release ${{ github.ref_name }}
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draft: true
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allowUpdates: true
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artifactErrorsFailBuild: true
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artifacts: pileupCaller-conda-linux
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artifactContentType: application/octet-stream

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