no qualimap and no R packages

Author: jen-reeve

docker/Dockerfile

@@ -159,33 +159,33 @@ RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11
 #create a symlink for python as hisat2 hashbangs are set for python and not python3
 RUN ln -s /usr/bin/python3 /usr/bin/python 
 
-# install R packages
-RUN Rscript -e 'install.packages("BiocManager", repos = "https://cloud.r-project.org")' \
-    && Rscript -e 'BiocManager::install("limma")' \
-    && Rscript -e 'BiocManager::install("edgeR")' \
-    && Rscript -e 'BiocManager::install("DESeq2")' \
-    && Rscript -e 'install.packages("beeswarm")' \
-    && Rscript -e 'install.packages("knitr")' \
-    && Rscript -e 'install.packages("gplots")' \
-    && Rscript -e 'BiocManager::install("goseq")' \
-    && Rscript -e 'BiocManager::install("GO.db")' \
-    && Rscript -e 'BiocManager::install("org.Sc.sgd.db")' \
-    && Rscript -e 'install.packages("ggiraph")' \
-    && Rscript -e 'install.packages("plotly")'
-
-# confirm all R packages load
-RUN Rscript -e 'library(BiocManager)' \
-    && Rscript -e 'library(limma)' \
-    && Rscript -e 'library(edgeR)' \
-    && Rscript -e 'library(DESeq2)' \
-    && Rscript -e 'library(beeswarm)' \
-    && Rscript -e 'library(knitr)' \
-    && Rscript -e 'library(gplots)' \
-    && Rscript -e 'library(goseq)' \
-    && Rscript -e 'library(GO.db)' \
-    && Rscript -e 'library(org.Sc.sgd.db)' \
-    && Rscript -e 'library(ggiraph)' \
-    && Rscript -e 'library(plotly)'
+# # install R packages
+# RUN Rscript -e 'install.packages("BiocManager", repos = "https://cloud.r-project.org")' \
+#     && Rscript -e 'BiocManager::install("limma")' \
+#     && Rscript -e 'BiocManager::install("edgeR")' \
+#     && Rscript -e 'BiocManager::install("DESeq2")' \
+#     && Rscript -e 'install.packages("beeswarm")' \
+#     && Rscript -e 'install.packages("knitr")' \
+#     && Rscript -e 'install.packages("gplots")' \
+#     && Rscript -e 'BiocManager::install("goseq")' \
+#     && Rscript -e 'BiocManager::install("GO.db")' \
+#     && Rscript -e 'BiocManager::install("org.Sc.sgd.db")' \
+#     && Rscript -e 'install.packages("ggiraph")' \
+#     && Rscript -e 'install.packages("plotly")'
+
+# # confirm all R packages load
+# RUN Rscript -e 'library(BiocManager)' \
+#     && Rscript -e 'library(limma)' \
+#     && Rscript -e 'library(edgeR)' \
+#     && Rscript -e 'library(DESeq2)' \
+#     && Rscript -e 'library(beeswarm)' \
+#     && Rscript -e 'library(knitr)' \
+#     && Rscript -e 'library(gplots)' \
+#     && Rscript -e 'library(goseq)' \
+#     && Rscript -e 'library(GO.db)' \
+#     && Rscript -e 'library(org.Sc.sgd.db)' \
+#     && Rscript -e 'library(ggiraph)' \
+#     && Rscript -e 'library(plotly)'
 
 # Set up environment variables for the virtual environment
 ENV PATH="/opt/venv/bin:$PATH"