diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml index e19efae..a5f310d 100644 --- a/.github/workflows/render-rmarkdown.yaml +++ b/.github/workflows/render-rmarkdown.yaml @@ -4,54 +4,53 @@ 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} - - name: Install packages for tutorial - run: | - devtools::install_github("immunogenomics/harmony") - BiocManager::install("Nebulosa") - BiocManager::install("JASPAR2020") - BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") - BiocManager::install("EnsDb.Hsapiens.v86") - devtools::install_github("CostaLab/MOJITOO") - install.packages('ggraph') - install.packages('igraph') - shell: Rscript {0} - - name: Install scMEGA - run: | - devtools::install_github("CostaLab/scMEGA") - shell: Rscript {0} +# jobs: +# render-rmarkdown: +# runs-on: ubuntu-latest +# env: +# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} +# steps: +# - uses: actions/checkout@v3 +# - uses: r-lib/actions/setup-pandoc@v2 +# - uses: r-lib/actions/setup-r@v2 +# - name: Install libraries +# run: | +# sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev +# sudo apt-get install libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev + # - name: Install dependencies + # run: | + # install.packages("textshaping") + # install.packages("curl") + # install.packages("devtools") + # install.packages("BiocManager") + # install.packages("rmarkdown") + # devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories()) + # devtools::install_github("satijalab/seurat", "seurat5") + # install.packages("Signac") + # BiocManager::install("destiny") + # shell: Rscript {0} + # - name: Install packages for tutorial + # run: | + # devtools::install_github("immunogenomics/harmony") + # BiocManager::install("Nebulosa") + # BiocManager::install("JASPAR2020") + # BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") + # BiocManager::install("EnsDb.Hsapiens.v86") + # devtools::install_github("CostaLab/MOJITOO") + # install.packages('ggraph') + # install.packages('igraph') + # shell: Rscript {0} + # - name: Install scMEGA + # run: | + # devtools::install_github("CostaLab/scMEGA") + # shell: Rscript {0} # - name: Render Rmarkdown files # run: | # pkgdown::build_site() # shell: Rscript {0} - - name: Commit files - run: | - git config --local user.name "$GITHUB_ACTOR" - git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" - git commit -am "Re-build Rmarkdown files" - git push origin || echo "No changes to commit" + # - name: Commit files + # run: | + # git config --local user.name "$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"