diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml index a5f310d..e530e19 100644 --- a/.github/workflows/render-rmarkdown.yaml +++ b/.github/workflows/render-rmarkdown.yaml @@ -4,31 +4,31 @@ name: render-rmarkdown run-name: Rendering rmarkdown files on: [push] -# jobs: -# render-rmarkdown: -# runs-on: ubuntu-latest -# env: -# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} -# steps: -# - uses: actions/checkout@v3 -# - uses: r-lib/actions/setup-pandoc@v2 -# - uses: r-lib/actions/setup-r@v2 -# - name: Install libraries -# run: | -# sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev -# sudo apt-get install libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev - # - name: Install dependencies - # run: | - # install.packages("textshaping") - # install.packages("curl") - # install.packages("devtools") - # install.packages("BiocManager") - # install.packages("rmarkdown") - # devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) - # devtools::install_github("satijalab/seurat", "seurat5") - # install.packages("Signac") - # BiocManager::install("destiny") - # shell: Rscript {0} +jobs: + render-rmarkdown: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-r@v2 + - name: Install libraries + run: | + sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev + sudo apt-get install libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev + - name: Install dependencies + run: | + install.packages("textshaping") + install.packages("curl") + install.packages("devtools") + install.packages("BiocManager") + install.packages("rmarkdown") + devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) + devtools::install_github("satijalab/seurat", "seurat5") + install.packages("Signac") + BiocManager::install("destiny") + shell: Rscript {0} # - name: Install packages for tutorial # run: | # devtools::install_github("immunogenomics/harmony") @@ -40,17 +40,17 @@ on: [push] # install.packages('ggraph') # install.packages('igraph') # shell: Rscript {0} - # - name: Install scMEGA - # run: | - # devtools::install_github("CostaLab/scMEGA") - # shell: Rscript {0} - # - name: Render Rmarkdown files - # run: | - # pkgdown::build_site() - # shell: Rscript {0} - # - name: Commit files - # run: | - # git config --local user.name "$GITHUB_ACTOR" - # git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" - # git commit -am "Re-build Rmarkdown files" - # git push origin || echo "No changes to commit" + - name: Install scMEGA + run: | + devtools::install_github("CostaLab/scMEGA") + shell: Rscript {0} + - name: Render Rmarkdown files + run: | + pkgdown::build_site() + shell: Rscript {0} + - name: Commit files + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git commit -am "Re-build Rmarkdown files" + git push origin || echo "No changes to commit"