add genebass description #1219
Workflow file for this run
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| name: Build Bystro Perl Package | |
| on: [push, pull_request] | |
| jobs: | |
| test-perl-package: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: perldocker/perl-tester:latest | |
| steps: | |
| - name: Perl version | |
| run: perl -V | |
| - name: Install system dependencies | |
| shell: bash | |
| run: apt-get install --no-install-recommends -y lz4 | |
| # taken from https://github.com/docker-library/golang/blob/master/1.21/bullseye/Dockerfile | |
| # NOTES: 1) updated paths are not usable by the step | |
| # 2) if GOBIN is not set, which is the case here, `go install ...` installs binaries to ${HOME}/go/bin | |
| - name: Install Go | |
| shell: bash | |
| run: | | |
| set -eux; \ | |
| arch="$(dpkg --print-architecture)"; arch="${arch##*-}"; \ | |
| url=; \ | |
| case "$arch" in \ | |
| 'amd64') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-amd64.tar.gz'; \ | |
| sha256='1241381b2843fae5a9707eec1f8fb2ef94d827990582c7c7c32f5bdfbfd420c8'; \ | |
| ;; \ | |
| 'armel') \ | |
| export GOARCH='arm' GOARM='5' GOOS='linux'; \ | |
| ;; \ | |
| 'armhf') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-armv6l.tar.gz'; \ | |
| sha256='a1ddcaaf0821a12a800884c14cb4268ce1c1f5a0301e9060646f1e15e611c6c7'; \ | |
| ;; \ | |
| 'arm64') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-arm64.tar.gz'; \ | |
| sha256='fc90fa48ae97ba6368eecb914343590bbb61b388089510d0c56c2dde52987ef3'; \ | |
| ;; \ | |
| 'i386') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-386.tar.gz'; \ | |
| sha256='fb209fd070db500a84291c5a95251cceeb1723e8f6142de9baca5af70a927c0e'; \ | |
| ;; \ | |
| 'mips64el') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-mips64le.tar.gz'; \ | |
| sha256='a569ffbc88b4e14cf2682f65cec950460665e4392b0d78b8868b4718c979bda8'; \ | |
| ;; \ | |
| 'ppc64el') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-ppc64le.tar.gz'; \ | |
| sha256='3b0e10a3704f164a6e85e0377728ec5fd21524fabe4c925610e34076586d5826'; \ | |
| ;; \ | |
| 'riscv64') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-riscv64.tar.gz'; \ | |
| sha256='67d14d3e513e505d1ec3ea34b55641c6c29556603c7899af94045c170c1c0f94'; \ | |
| ;; \ | |
| 's390x') \ | |
| url='https://dl.google.com/go/go1.21.3.linux-s390x.tar.gz'; \ | |
| sha256='4c78e2e6f4c684a3d5a9bdc97202729053f44eb7be188206f0627ef3e18716b6'; \ | |
| ;; \ | |
| *) echo >&2 "error: unsupported architecture '$arch' (likely packaging update needed)"; exit 1 ;; \ | |
| esac; \ | |
| build=; \ | |
| if [ -z "$url" ]; then \ | |
| # https://github.com/golang/go/issues/38536#issuecomment-616897960 | |
| build=1; \ | |
| url='https://dl.google.com/go/go1.21.3.src.tar.gz'; \ | |
| sha256='186f2b6f8c8b704e696821b09ab2041a5c1ee13dcbc3156a13adcf75931ee488'; \ | |
| echo >&2; \ | |
| echo >&2 "warning: current architecture ($arch) does not have a compatible Go binary release; will be building from source"; \ | |
| echo >&2; \ | |
| fi; \ | |
| \ | |
| wget -O go.tgz.asc "$url.asc"; \ | |
| wget -O go.tgz "$url" --progress=dot:giga; \ | |
| echo "$sha256 *go.tgz" | sha256sum -c -; \ | |
| \ | |
| # https://github.com/golang/go/issues/14739#issuecomment-324767697 | |
| GNUPGHOME="$(mktemp -d)"; export GNUPGHOME; \ | |
| # https://www.google.com/linuxrepositories/ | |
| gpg --batch --keyserver keyserver.ubuntu.com --recv-keys 'EB4C 1BFD 4F04 2F6D DDCC EC91 7721 F63B D38B 4796'; \ | |
| # let's also fetch the specific subkey of that key explicitly that we expect "go.tgz.asc" to be signed by, just to make sure we definitely have it | |
| gpg --batch --keyserver keyserver.ubuntu.com --recv-keys '2F52 8D36 D67B 69ED F998 D857 78BD 6547 3CB3 BD13'; \ | |
| gpg --batch --verify go.tgz.asc go.tgz; \ | |
| gpgconf --kill all; \ | |
| rm -rf "$GNUPGHOME" go.tgz.asc; \ | |
| \ | |
| tar -C /usr/local -xzf go.tgz; \ | |
| rm go.tgz; | |
| /usr/local/go/bin/go version | |
| echo "/usr/local/go/bin" >> $GITHUB_PATH | |
| echo "${HOME}/go/bin" >> $GITHUB_PATH | |
| - name: Install one-off Bystro dependencies | |
| shell: bash | |
| run: | | |
| go install github.com/bystrogenomics/[email protected] | |
| cpm install -g https://github.com/bystrogenomics/msgpack-perl.git | |
| cpm install -g --no-test MouseX::Getopt | |
| git clone --depth 1 --recurse-submodules https://github.com/salortiz/LMDB_File.git \ | |
| && cd LMDB_File \ | |
| && cpanm --quiet . | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install Bystro dependencies | |
| run: | | |
| cd perl | |
| cpm install -g --show-build-log-on-failure $(dzil authordeps --missing) | |
| cpm install -g --show-build-log-on-failure $(dzil listdeps --missing) | |
| - name: Test Bystro | |
| run: cd perl && dzil test --all | |
| - name: Build Bystro tarball | |
| run: cd perl && dzil build |