Hi. I am wondering how to install bioconductor packages in graham?
I tried the following:
module load gcc/7.3.0
module load r/3.6.0
module load r-bundle-bioconductor/3.9
But it didn’t work.
Thanks for your help!
Do you need this specific version of DESeq2 or any version (the latest) is fine?
Any version would be fine. Thanks for answering.
BiocManager::install(“DESeq2”) will work. You do not have write permission to the software directory but you can use a personal library instead ‘~/R/x86_64-pc-linux-gnu-library/3.6’.
also, just to point out that the ‘module’ commands are unix commands that you can run on the command-line, while the ‘BiocManager::install’ command is an R command. So this needs to be run within R or in your R script.
if you try to run BiocManager on the unix command-line, it won’t recognize the command and will fail with the following:
> -bash: syntax error near unexpected token `”DESeq2″‘