Skip to content

Updated versions and minor corrections to rnaseq lab #205

Updated versions and minor corrections to rnaseq lab

Updated versions and minor corrections to rnaseq lab #205

Workflow file for this run

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