Update tutorial based on changes from singler #23
Workflow file for this run
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name: Quarto Publish | |
on: | |
push: | |
branches: [ master ] | |
pull_request: | |
branches: [ master ] | |
jobs: | |
build-deploy: | |
container: | |
image: bioconductor/bioconductor_docker:devel | |
runs-on: ubuntu-latest | |
permissions: | |
contents: write | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Install rsync | |
run: | | |
sudo apt-get update | |
sudo apt-get install -y rsync | |
# - name: Install curl | |
# run: | | |
# sudo apt-get install libcurl4-openssl-dev | |
# - name: Setup Quarto | |
# uses: quarto-dev/quarto-actions/setup@v2 | |
# with: | |
# tinytex: true | |
- name: Setup Quarto | |
run: | | |
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.43/quarto-1.5.43-linux-amd64.deb && \ | |
dpkg -i quarto-1.5.43-linux-amd64.deb && \ | |
rm quarto-1.5.43-linux-amd64.deb | |
- name: Setup tinytex | |
run: quarto install tinytex | |
# - name: Setup Python | |
# uses: actions/setup-python@v4 | |
# with: | |
# python-version: '3.9' | |
# cache: 'pip' | |
- name: Install Python dependencies | |
run: pip install -r requirements.txt | |
# - name: Setup R | |
# uses: r-lib/actions/setup-r@v2 | |
# with: | |
# r-version: '4.4.0' | |
- name: Set directories | |
run: | | |
echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV | |
- name: Restore the package directory | |
uses: actions/cache@v3 | |
with: | |
path: ${{ env.R_PKG_DIR }} | |
key: check-packages | |
- name: Install R packages | |
run: Rscript rpackages.R | |
# build SQLite from source, because I need 3.35<= | |
- name: Download SQLite3 | |
run: | | |
wget https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz | |
tar -xvf sqlite-autoconf-3450300.tar.gz | |
- name: Install SQLite3 | |
run: | | |
cd sqlite-autoconf-3450300 | |
./configure | |
make | |
sudo make install | |
export PATH="/usr/local/lib:$PATH" | |
cd .. | |
- name: Quarto render | |
run: | | |
quarto render --execute --to html --output-dir ./build | |
env: | |
LD_LIBRARY_PATH: /usr/local/lib | |
- name: Create nojekyll | |
run: touch ./build/.nojekyll | |
- name: GH Pages Deployment | |
# if: github.ref == 'refs/heads/master' | |
uses: JamesIves/github-pages-deploy-action@v4 | |
with: | |
branch: gh-pages # The branch the action should deploy to. | |
folder: ./build | |
clean: true # Automatically remove deleted files from the deploy branch |