Control R environment using modules - Revision history

Dawes001: /* See also */

2018-05-23T08:47:06Z

2013-11-29T22:59:12Z

← Older revision		Revision as of 00:59, 30 November 2013
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	== See also ==		== See also ==

			* [[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 ==		== External links ==

2013-11-29T22:57:56Z

← Older revision		Revision as of 00:57, 30 November 2013
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	== Load Module ==		== Load Module ==

			<source lang='bash'>
			module avail
			</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'>
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	</source>		</source>

	~~== Install R package and check install path ==~~

	> installed.packages()		> installed.packages()

2013-11-29T22:56:22Z

← Older revision		Revision as of 00:56, 30 November 2013
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			== Setting up a semi-public repository ==

	<source lang='bash'>		<source lang='bash'>
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	</source>		</source>
	Note: need to do this only once per version; make sure that the folder does not already exist.		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'>
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	</source>		</source>

			== Load Module ==

	----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------		----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
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	install.packages('car')		install.packages('car')
	</source>		</source>

			== Install R package and check install path ==

	> 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 ==

			== External links ==

2013-11-29T22:54:12Z

← Older revision		Revision as of 00:54, 30 November 2013
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	<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.		Note: need to do this only once per version; make sure that the folder does not already exist.

2013-11-29T22:53:39Z

← Older revision		Revision as of 00:53, 30 November 2013
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	/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/		/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.

	<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'>

2013-11-29T22:50:11Z

← Older revision		Revision as of 00:50, 30 November 2013
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	<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/
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	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>		</source>

2013-11-29T22:48:04Z

2013-11-29T22:47:21Z

← Older revision		Revision as of 00:47, 30 November 2013
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	----------------------------------- /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='r'>
			install.packages('car')
			</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"

2013-11-29T22:46:02Z

← Older revision		Revision as of 00:46, 30 November 2013
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	----------------------------------- /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

			> installed.packages()
			Package LibPath
			car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"

← Older revision		Revision as of 10:47, 23 May 2018
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	== See also ==		== 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]]		* [[Domain_specific_software_on_B4Fcluster_installation_by_users \| Installing domain specific software: installation by users]]
	* [[Setting local variables]]		* [[Setting local variables]]