FORUMInstalling bioconductor package
Matt asked 6 months ago



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
BiocManager::install(“DESeq2-1.22.1”)

But it didn’t work.

Thanks for your help!

1 Answers
zhibin Staff answered 6 months ago



Do you need this specific version of DESeq2 or any version (the latest) is fine?

Matt replied 6 months ago

Any version would be fine. Thanks for answering.

zhibin Staff replied 6 months ago

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’.

jrosner Staff replied 6 months ago

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″‘

Matt replied 6 months ago

Thank you!