Update variant calling lab for Dardel #251
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| env: | |
| REGISTRY: ghcr.io | |
| ORG: nbisweden | |
| IMAGE: workshop-ngsintro:latest | |
| jobs: | |
| quarto-render-job: | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Set time zone | |
| uses: szenius/[email protected] | |
| with: | |
| timezoneLinux: "Europe/Stockholm" | |
| timezoneMacos: "Europe/Stockholm" | |
| timezoneWindows: "W. Europe Standard Time" | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Pull image | |
| run: docker pull ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} | |
| - name: Define variables | |
| run: | | |
| echo "PATH_REPO=$(pwd)" >> $GITHUB_ENV | |
| echo "PATH_EXPORT=$(grep -E 'output-dir' _quarto.yml | xargs | sed 's/output-dir://' | xargs)" >> $GITHUB_ENV | |
| echo "REPO=$(basename ${GITHUB_REPOSITORY})" >> $GITHUB_ENV | |
| - name: Check docker and variables | |
| run: | | |
| docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/qmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} Rscript -e "print('R in docker works!')" | |
| echo "GITHUB_ACTOR: ${GITHUB_ACTOR}" | |
| echo "GITHUB_REPOSITORY: ${GITHUB_REPOSITORY}" | |
| echo "REPO: ${REPO}" | |
| echo "env.PATH_REPO: ${{ env.PATH_REPO }}" | |
| echo "PATH_EXPORT: ${PATH_EXPORT}" | |
| echo "GITHUB_REPOSITORY_OWNER: ${GITHUB_REPOSITORY_OWNER}" | |
| echo "---------------------------------------------------------------------------------------------" | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| echo "---------------------------------------------------------------------------------------------" | |
| printenv | |
| sed --version | |
| - name: Render site, pull repo, copy folder, create index, push repo | |
| run: | | |
| # Add git info | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "gh_action" | |
| # Render website | |
| echo "Rendering qmd files ..." | |
| echo "PWD: ${PWD}" | |
| ls -l . | |
| docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/qmd ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} | |
| # List folder contents | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| echo "Folder contents at ${PATH_REPO}/${PATH_EXPORT}:" | |
| ls -lh ${PATH_REPO}/${PATH_EXPORT} | |
| # Clone gh-pages branch and remove old directories with same name | |
| git clone --depth 1 --single-branch --branch gh-pages "https://${{ secrets.TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo | |
| cd tmprepo | |
| if [ -d ${PATH_EXPORT} ]; then | |
| echo "Directory ${PATH_EXPORT} already exists. Removing the directory." | |
| git rm -r ${PATH_EXPORT} | |
| git commit -m "Old directory ${PATH_EXPORT} deleted." | |
| fi | |
| cd ${PATH_REPO} | |
| cp -r ${PATH_EXPORT} tmprepo/ | |
| cd tmprepo | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| # create index file | |
| printf "<div class='wrapper-logo'><img class='logo' src='assets/logo.svg'></div>" > index.md | |
| printf "The current and all previous instances of this workshop are listed below.\n" >> index.md | |
| printf "<hr>\n" >> index.md | |
| printf "<div class='workshop-list'>\n" >> index.md | |
| dirs=$(ls -d [0-9]*[0-9]/ | sed 's/\///' | tac) | |
| for i in ${dirs[@]} | |
| do | |
| if [ ${i:2:2} -lt 1 ] || [ ${i:2:2} -gt 12 ] | |
| then echo "Month: ${i:2:2}. Last 2 values in output_dir must be a month between 01 and 12." | |
| fi | |
| # This code works for year 2000 and later | |
| printf -v thedate '2000-01-01 +%s years +%s months -1 day' "${i:0:2}" "${i:2}" | |
| dt=$(date -d "$thedate" +'%Y %b') | |
| echo $dt | |
| printf "<h3><a href='https://${GITHUB_REPOSITORY_OWNER}.github.io/${REPO}/${i}/'>$dt</a></h3>" >> index.md | |
| done | |
| printf "</div>\n" >> index.md | |
| # printf "<hr>\n" >> index.md | |
| # printf "$(date +'%Y') • NBIS\n" >> index.md | |
| echo "Folder contents at $(pwd):" | |
| ls -lh | |
| # Push changes back | |
| git add . | |
| git commit -m "Updated contents at $(date +%Y%m%d-%H%M%S)" | |
| git push origin |