update workflow

CostaLab · Jul 4, 2024 · 08148a6 · 08148a6
1 parent 7292233
commit 08148a6
Showing 1 changed file with 46 additions and 47 deletions.
diff --git 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"