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Revision 1 as of 2020-04-24 07:21:07

Installing software

Installing software or pipeline can be a difficult task to accomplish. Therefore we suggest all users to make the programs they installed available to all users whenever it is possible. In general programs/pipelines that should be available to all are installed in /tools folder. On this page will be described how to make tools available on our system for installation procedure of your specific program please refer to the instructions coming with that program.

Who can install software

In principle any users except students and guests should be able to install bioinfo tools in folders made for that purpose.

Install R packages

  • Packages for R are installed within R, so to install R packages, you will first need to load the module R and run R. 

module load R
R

  • Use the following R command to print where are the R libraries. Users libraries are installed in /tools/R_libs/3.6.1 

.libPaths()
#[1] "/tools/R_libs/3.6.1"                            
#[2] "/opt/ohpc/pub/libs/gnu8/R/3.6.1/lib64/R/library"
  • To see all available/installed packages 

.packages(all.available=T)

  • To install R packages and dependancies. Installation will automatically be done in a /tools/R_libs/3.6.1 if permissions allows it. If not you could be asked to create a private one. 

install.packages(c("<package1>", "<package2>,..."), dep=T)

  • To install BIOINFORMATICS R PACKAGES, we recommend to use "bioconductor" channels. 

library(BiocManager)
BiocManager::install(c("<package1>", "<package2>",...))

Read more about R and bioconductor: