use pak in base_extra

facilebio · Sep 17, 2024 · 4319c36 · 4319c36
1 parent 00a392b
commit 4319c36
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/facilebio_base_extra/Dockerfile b/facilebio_base_extra/Dockerfile
@@ -5,12 +5,20 @@ LABEL maintainer="Steve Lianoglou ([email protected])"
 # Installs R packages not available/released on the standard channels
 # (bioconductor / CRAN)
 
+# RUN --mount=type=secret,id=GITHUB_PAT \
+#     GITHUB_PAT=$(cat /run/secrets/GITHUB_PAT) \
+#     Rscript -e "library(BiocManager); install(c(\
+#         'lianos/sparrow', \
+#         'lianos/sparrow.shiny' \
+#     ))" \
+#     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
 RUN --mount=type=secret,id=GITHUB_PAT \
     GITHUB_PAT=$(cat /run/secrets/GITHUB_PAT) \
-    Rscript -e "library(BiocManager); install(c(\
+    Rscript -e "pak::pkg_install(c(\
         'lianos/sparrow', \
         'lianos/sparrow.shiny' \
-    ))" \
+    ), upgrade = TRUE, ask = FALSE)" \
     && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
 
 # Init command for s6-overlay