Change to Perl versions from Perlbrew

.github/workflows/perlbrew.sha256

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+c3996e4fae37a0ae01839cdd73752fb7b17e81bac2a8b39712463a7d518c4945  perlbrew.sh

.github/workflows/run-tests.yml

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+name: "Unit tests"
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l -e -o pipefail {0}
+
+    env:
+      PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
+      NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
+      WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic"
+      CONDA_TEST_ENV: test-environment
+      NPM_CONFIG_PREFIX: "$HOME/.npm-global"
+      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
+      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        perl: ["5.26.3", "5.34.1"]
+        node: ['14.8.0']
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: "Install OS dependencies"
+        run: |
+          sudo apt-get update
+          # https://github.com/actions/runner-images/issues/2139
+          sudo apt-get remove -y nginx libgd3
+          sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl
+
+      - name: "Initialize Miniconda"
+        run: |
+          echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile"
+
+      - name: "Cache Conda"
+        id: minicondaCache
+        uses: actions/cache@v3
+        with:
+          path: |
+            ~/conda/pkgs
+            ~/conda/envs
+          key: ${{ runner.os }}-build-miniconda
+
+      - name: "Install Conda packages"
+        env:
+          CONDA_TEST_ENV: test-environment
+        run: |
+          conda config --prepend pkgs_dirs ~/conda/pkgs
+          conda config --prepend envs_dirs ~/conda/envs
+
+          conda config --set auto_update_conda False
+          conda config --prepend channels "$WSI_CONDA_CHANNEL"
+          conda config --append channels conda-forge
+          conda info
+
+          conda create -y -n "$CONDA_TEST_ENV"
+          conda install -y -n "$CONDA_TEST_ENV" nodejs=="${{ matrix.node }}"
+          conda install -y -n "$CONDA_TEST_ENV" npg_qc_utils
+          conda install -y -n "$CONDA_TEST_ENV" baton
+
+      - name: "Cache Perl"
+        id: cache-perl
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.PERL_CACHE }}
+          key: ${{ runner.os }}-${{ matrix.perl }}-perl
+
+      - name: "Install Perlbrew"
+        if: steps.cache-perl.outputs.cache-hit != 'true'
+        run: |
+          curl -sSL https://install.perlbrew.pl -o perlbrew.sh
+          sha256sum -c .github/workflows/perlbrew.sha256
+          export PERLBREW_ROOT=${{ env.PERL_CACHE }}
+          sh perlbrew.sh
+          
+          source ${{ env.PERL_CACHE }}/etc/bashrc
+          perlbrew available
+          perlbrew install --notest perl-${{ matrix.perl }}
+          perlbrew use perl-${{ matrix.perl }}
+          perlbrew install-cpanm
+
+      - name: "Initialize Perlbrew"
+        run: |
+          echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile"
+
+      - name: "NPM"
+        run: |
+          mkdir -p "$NPM_CONFIG_PREFIX"
+          ${GITHUB_WORKSPACE}/scripts/before_install.sh
+
+      - name: "Install Perl dependencies"
+        run: |
+          cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          
+          cpanm --quiet --notest Alien::Tidyp
+          cpanm --quiet --notest LWP::Protocol::https
+          cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz
+    
+          ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
+             perl-dnap-utilities \
+             ml_warehouse \
+             npg_tracking \
+             npg_seq_common \
+             perl-irods-wrap
+
+          cpanm --installdeps --notest .
+
+          pushd npg_qc_viewer
+          export PERL5LIB="$PERL5LIB:../lib"
+          cpanm --notest --installdeps .
+
+      - name: "Log install failure"
+        if: ${{ failure() }}
+        run: |
+          find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;
+
+      - name: "Archive CPAN logs on failure"
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: cpan_log
+          path: ~/.cpanm/work/*/build.log
+          retention-days: 5
+
+      - name: "Run tests"
+        run: |
+          conda activate "$CONDA_TEST_ENV"
+          conda info --envs
+          
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
+          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
+          
+          export PATH=$HOME/.nvm/versions/node/v${{ matrix.node }}/bin:$PATH
+          export TEST_AUTHOR=1
+          export WTSI_NPG_iRODS_Test_Resource=testResc
+          export WTSI_NPG_iRODS_Test_IRODS_ENVIRONMENT_FILE=$HOME/.irods/irods_environment.json
+          
+          perl Build.PL
+          ./Build test --verbose
+          ./Build install
+  
+          pushd npg_qc_viewer
+          export PERL5LIB="$PERL5LIB:../lib"
+          perl Build.PL --installjsdeps
+          ./Build
+          ./Build test --verbose
+          $(npm bin)/grunt -v

scripts/install_wsi_dependencies.sh

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+#!/bin/bash
+
+set -e -u -x
+
+WSI_NPG_GITHUB_URL=${WSI_NPG_GITHUB_URL:=https://github.com/wtsi-npg}
+WSI_NPG_BUILD_BRANCH=${WSI_NPG_BUILD_BRANCH:=devel}
+
+# The first argument is the install base for NPG modules, enabling them to be
+# installed independently of CPAN dependencies. E.g. for cases where we want
+# different caching behaviour.
+NPG_ROOT="$1"
+shift
+
+repos=""
+for repo in "$@" ; do
+    cd /tmp
+
+    # Clone deeper than depth 1 to get the tag even if something has been already
+    # committed over the tag
+    git clone --branch master --depth 3 "$WSI_NPG_GITHUB_URL/${repo}.git" "${repo}.git"
+    cd "/tmp/${repo}.git"
+
+    # Shift off master to appropriate branch (if possible)
+    git ls-remote --heads --exit-code origin "$WSI_NPG_BUILD_BRANCH" && \
+	    git pull origin "$WSI_NPG_BUILD_BRANCH" && \
+	    echo "Switched to branch $WSI_NPG_BUILD_BRANCH"
+    repos="$repos /tmp/${repo}.git"
+done
+
+# Install CPAN dependencies. The src libs are on PERL5LIB because of
+# circular dependencies. The blibs are on PERL5LIB because the package
+# version, which cpanm requires, is inserted at build time. They must
+# be before the libs for cpanm to pick them up in preference.
+for repo in $repos
+do
+    export PERL5LIB="$PERL5LIB:$repo/blib/lib:$repo/lib"
+done
+
+for repo in $repos
+do
+    cd "$repo"
+    cpanm --quiet --notest --installdeps .
+    perl Build.PL
+    ./Build
+done
+
+# Finally, bring any common dependencies up to the latest version and
+# install
+for repo in $repos
+do
+    cd "$repo"
+    cpanm --quiet --notest --installdeps .
+    ./Build install --install-base "$NPG_ROOT"
+done