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