= 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:
 * https://cran.r-project.org/
 * https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf
 * https://www.bioconductor.org/