Control R environment using modules: Difference between revisions
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== Setting up a semi-public repository == | |||
<source lang='bash'> | <source lang='bash'> | ||
/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2 | mkdir /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2 | ||
</source> | </source> | ||
Note: need to do this only once per version; make sure that the folder does not already exist. | |||
== Create an R module == | |||
<source lang='bash'> | <source lang='bash'> | ||
mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/ | mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/ | ||
</source> | </source> | ||
Note: need to do this only once per version; make sure that the folder does not already exist. | |||
<source lang='bash'> | <source lang='bash'> | ||
cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur | cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur | ||
</source> | </source> | ||
Note: need to do this only once per version; make sure that the file does not already exist. | |||
<source lang='tcl'> | <source lang='tcl'> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## R3 modulefile | ## R3 modulefile modified for WUR/ABGC use | ||
## | ## | ||
proc ModulesHelp { } { | proc ModulesHelp { } { | ||
puts stderr "\tAdds R v3.0.2 to your environment" | puts stderr "\tAdds R v3.0.2 to your environment and sets WUR/ABGC libraries" | ||
} | } | ||
module-whatis "Adds R v3.0.2 to your environment" | module-whatis "Adds R v3.0.2 to your environment and set WUR/ABGC libraries" | ||
set r3_root /cm/shared/apps/R3/ | set r3_root /cm/shared/apps/R3/ | ||
| Line 29: | Line 36: | ||
prepend-path LD_LIBRARY_PATH $r3_root/lib64 | prepend-path LD_LIBRARY_PATH $r3_root/lib64 | ||
prepend-path R_LIBS_SITE $r3_wur_root | prepend-path R_LIBS_SITE $r3_wur_root | ||
</source> | |||
== Load Module == | |||
<source lang='bash'> | |||
module avail | |||
</source> | </source> | ||
----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles ----------------------------------- | ----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles ----------------------------------- | ||
bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur | bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur | ||
<source lang='bash'> | |||
module load R/3.0.2_wur | |||
</source> | |||
== Install R package and check install path == | |||
<source lang='rsplus'> | <source lang='rsplus'> | ||
install.packages('car') | install.packages('car') | ||
</source> | </source> | ||
> installed.packages() | > installed.packages() | ||
Package LibPath | Package LibPath | ||
car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2" | car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2" | ||
== See also == | |||
* [[Parallel_R_code_on_SLURM | Running parallel workloads in R on Slurm]] | |||
* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]] | |||
* [[Setting local variables]] | |||
* [[Installing_R_packages_locally | Installing R packages locally]] | |||
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]] | |||
== External links == | |||
Latest revision as of 09:47, 23 May 2018
Setting up a semi-public repository
<source lang='bash'> mkdir /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2 </source> Note: need to do this only once per version; make sure that the folder does not already exist.
Create an R module
<source lang='bash'> mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/ </source> Note: need to do this only once per version; make sure that the folder does not already exist.
<source lang='bash'> cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur </source> Note: need to do this only once per version; make sure that the file does not already exist.
<source lang='tcl'>
- %Module1.0#######################################################################
- R3 modulefile modified for WUR/ABGC use
proc ModulesHelp { } {
puts stderr "\tAdds R v3.0.2 to your environment and sets WUR/ABGC libraries"
}
module-whatis "Adds R v3.0.2 to your environment and set WUR/ABGC libraries"
set r3_root /cm/shared/apps/R3/ set r3_wur_root /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/
prepend-path PATH $r3_root/bin prepend-path MANPATH $r3_root/share/man prepend-path LD_LIBRARY_PATH $r3_root/lib64 prepend-path R_LIBS_SITE $r3_wur_root
</source>
Load Module
<source lang='bash'> module avail </source>
----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles ----------------------------------- bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur
<source lang='bash'> module load R/3.0.2_wur </source>
Install R package and check install path
<source lang='rsplus'> install.packages('car') </source>
> installed.packages()
Package LibPath
car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"
See also
- Running parallel workloads in R on Slurm
- Installing domain specific software: installation by users
- Setting local variables
- Installing R packages locally
- Setting up and using a virtual environment for Python3