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@@ -4,54 +4,53 @@ name: render-rmarkdown | |
| run-name: Rendering rmarkdown files | ||
| on: [push] | ||
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| 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 "[email protected]" | ||
| 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 "[email protected]" | ||
| # git commit -am "Re-build Rmarkdown files" | ||
| # git push origin || echo "No changes to commit" | ||