diff --git a/.github/workflows/render_page.yml b/.github/workflows/render_page.yml index 0f59f2f..cf64328 100644 --- a/.github/workflows/render_page.yml +++ b/.github/workflows/render_page.yml @@ -38,11 +38,6 @@ jobs: - name: Install R and setup-renv uses: r-lib/actions/setup-r@v2 - - name: Set up renv - uses: r-lib/actions/setup-renv@v2 - with: - profile: 'ci' # Use the 'ci' profile - # - name: Check renv paths # run: | # Rscript -e 'cat("Project Library:", renv::paths$library(), "\n")' @@ -53,23 +48,16 @@ jobs: # - name: Install R Dependencies # uses: r-lib/actions/setup-renv@v2 - - - name: Extra packages + + - name: installations run: | - R -e 'install.packages(c("devtools", "rmarkdown", "markdown", "knitr"))' + R -e 'install.packages(c("devtools", "remotes", "BiocManager", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' R -e 'devtools::install_github("stephenturner/annotables")' + R -e 'remotes::install_github("ctlab/fgsea")' + R -e 'BiocManager::install(c("DESeq2", "clusterProfiler", "DOSE", "org.Hs.eg.db", "pathview", "DEGreport", "tximport", "AnnotationHub", "ensembldb","apeglm","ggnewscale"))' + R -e 'install.packages(c("rmarkdown", "markdown", "knitr"))' env: GITHUB_PAT: ${{ secrets.TOKEN }} - -# - name: installations -# run: | -# R -e 'install.packages(c("devtools"))' -# R -e 'install.packages(c("devtools", "BiocManager", "tidyverse", "RColorBrewer", "pheatmap", "ggrepel", "cowplot"))' -# R -e 'devtools::install_github("stephenturner/annotables")' -# R -e 'BiocManager::install(c("DESeq2", "clusterProfiler", "DOSE", "org.Hs.eg.db", "pathview", "DEGreport", "tximport", "AnnotationHub", "ensembldb","apeglm","ggnewscale"))' -# R -e 'install.packages(c("rmarkdown", "markdown", "knitr"))' -# env: -# GITHUB_PAT: ${{ secrets.TOKEN }} - name: Pull Notebooks folder content if: runner.os == 'Linux'