Globally installed software - Revision history

Dawes0011 at 08:58, 16 June 2023

2023-06-16T08:58:33Z

← Older revision		Revision as of 10:58, 16 June 2023
Line 110:		Line 110:
	== Available as global SHARED modules ==		== Available as global SHARED modules ==
	Software can be deposited in:		Software can be deposited in:
	~~/cm~~/shared/apps/SHARED/		/shared/apps/SHARED/

	Modules can be found in:		Modules can be found in:
	~~/cm~~/shared/modulefiles/SHARED/		/shared/modulefiles/SHARED/

	{\| width="90%"		{\| width="90%"
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	<pre>		<pre>
	export MODULEPATH=$MODULEPATH:~~/cm~~/shared/apps/WUR/ABGC/modulefiles		export MODULEPATH=$MODULEPATH:/shared/apps/WUR/ABGC/modulefiles
	</pre>		</pre>
	This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again:		This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again:
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	This should give output that includes something similar to this:		This should give output that includes something similar to this:

	---------------------------------------- ~~/cm~~/shared/modulefiles/ -----------------------------------------		---------------------------------------- /shared/modulefiles/ -----------------------------------------
	ALLPATHS-LG/48961 bwa/0.7.5a jellyfish/2.1.1 RepeatMasker/4.0.3		ALLPATHS-LG/48961 bwa/0.7.5a jellyfish/2.1.1 RepeatMasker/4.0.3
	augustus/2.7 cegma/2.4 MAFFT/7.130 RepeatModeler/1.0.7		augustus/2.7 cegma/2.4 MAFFT/7.130 RepeatModeler/1.0.7

Prins0891: to

 to fix code blocks

2023-06-15T14:50:07Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:50, 15 June 2023
Line 166:		Line 166:
	To allow the <code>module</code> program to find the custom module directory, the location of that directory has to be added to <code>MODULEPATH</code> variable.		To allow the <code>module</code> program to find the custom module directory, the location of that directory has to be added to <code>MODULEPATH</code> variable.

	<~~source lang='bash'~~>		<pre>
	export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles		export MODULEPATH=$MODULEPATH:/cm/shared/apps/WUR/ABGC/modulefiles
	</~~source~~>		</pre>
	This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again:		This can be made permanent by adding this line of code to the <code>.bash_profile</code> file in the root of your home folder. To then load the modified <code>MODULEPATH</code> variable you have to load <code>.bash_profile</code> again:
	<~~source lang='bash'~~>		<pre>
	source .bash_profile		source .bash_profile
	</~~source~~>		</pre>
	This needs to be done only for terminals that are already open. Next time you login, <code>.bash_profile</code> will be loaded automatically.		This needs to be done only for terminals that are already open. Next time you login, <code>.bash_profile</code> will be loaded automatically.

	You can check if the modules are found.		You can check if the modules are found.
	<~~source lang='bash'~~>		<pre>
	module avail		module avail
	</~~source~~>		</pre>
	This should give output that includes something similar to this:		This should give output that includes something similar to this:

Dawes001 at 13:46, 19 March 2019

2019-03-19T13:46:43Z

← Older revision		Revision as of 15:46, 19 March 2019
Line 191:		Line 191:

	== See also ==		== See also ==
	* [[~~Main_Page#Using_the_B4F_Cluster \| Using the B4F Cluster]]~~		* [[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]]
	* [[Installing_R_packages_locally \| Installing R packages locally]]		* [[Installing_R_packages_locally \| Installing R packages locally]]

Dawes001: /* Available as modules */

2017-08-24T14:24:10Z

Available as modules

← Older revision		Revision as of 16:24, 24 August 2017
Line 11:		Line 11:
	* boost		* boost
	* [[bowtie2 \| bowtie]]		* [[bowtie2 \| bowtie]]
	* canu		* [[canu \| canu]]
	* cdo		* cdo
	* cmgui		* cmgui
			* [[cuda \| cuda]]
	* diamond		* diamond
	* [[dmtcp \| dmtcp]]		* [[dmtcp \| dmtcp]]

Dawes001 at 13:26, 21 August 2017

2017-08-21T13:26:34Z

← Older revision		Revision as of 15:26, 21 August 2017
Line 53:		Line 53:
	* julia		* julia
	* lapack		* lapack
	* matlab		* [[matlab \| MATLAB]]
	* mixblup		* mixblup
	* mpich		* mpich

Dawes001 at 09:31, 7 August 2017

2017-08-07T09:31:10Z

← Older revision		Revision as of 11:31, 7 August 2017
Line 15:		Line 15:
	* cmgui		* cmgui
	* diamond		* diamond
	* dmtcp		* [[dmtcp \| dmtcp]]
	* emos		* emos
	* fasttree		* fasttree

Dawes001 at 10:49, 11 July 2017

2017-07-11T10:49:57Z

← Older revision		Revision as of 12:49, 11 July 2017
Line 36:		Line 36:
	* grib		* grib
	* gsl		* gsl
	* hadoop		* [[hadoop \| hadoop ]]
	* hdf4		* hdf4
	* hdf5		* hdf5

Dawes001 at 15:30, 19 June 2017

2017-06-19T15:30:23Z

← Older revision		Revision as of 17:30, 19 June 2017
Line 7:		Line 7:
	* blacs		* blacs
	* blas		* blas
	* BLAST+		* [[BLAST \| BLAST+]]
	* bonnie++		* bonnie++
	* boost		* boost
	* bowtie		* [[bowtie2 \| bowtie]]
	* canu		* canu
	* cdo		* cdo
Line 39:		Line 39:
	* hdf4		* hdf4
	* hdf5		* hdf5
	* ~~hdf5_18~~		* [[hmmer \| hmmer]]
	* hmmer
	* hpl		* hpl
	* htslib		* htslib
Line 75:		Line 74:
	* openmpi		* openmpi
	* oracle-instantclient		* oracle-instantclient
	* pbspro
	* phdf5		* phdf5
	* picard		* picard
Line 83:		Line 81:
	* R		* R
	* ragel		* ragel
	* RAxML		* [[RAxML \| RAxML]]
	* RRO		* RRO
	* rstudio		* rstudio
	* samtools		* [[samtools \| samtools]]
	* scalapack		* scalapack
	* sge
	* SHARED
	* slurm		* slurm
	* slurm-drmaa		* slurm-drmaa
	* snpEff		* snpEff
	* spark		* [[spark \| SPARK]]
	* szip		* szip
	* torque		* torque
	* trinity		* [[Trinity \| trinity]]
	* udunits		* udunits
	* vcftools		* vcftools
	* vim		* vim
	* zlib		* zlib

	== Globally installed on all nodes ==		== Globally installed on all nodes ==

Dawes001 at 15:24, 19 June 2017

2017-06-19T15:24:26Z

@@ Line 1: / Line 1: @@
 == Available as modules ==
-* gcc/4.8.1
+* acml
-* python/2.7.6
+* alphaimpute
-* python/3.3.3
+* bamtools
-* R/3.0.2
+* bcftools
+* beagle
 == Globally installed on all nodes ==

Herre011: /* Available as global SHARED modules */

2015-02-05T14:42:42Z

Available as global SHARED modules

← Older revision		Revision as of 16:42, 5 February 2015
Line 26:		Line 26:
	* [[allpathslg_48961 \| ALLPATHS-LG/48961]]		* [[allpathslg_48961 \| ALLPATHS-LG/48961]]
	* [[allpathslg 51910 \| ALLPATHS-LG/51910]]		* [[allpathslg 51910 \| ALLPATHS-LG/51910]]
			* [[ANGSD_0.614 \| angsd/0.614]]
	* [[augustus_2.7 \| augustus/2.7]]		* [[augustus_2.7 \| augustus/2.7]]
	* [[bedtools2.18 \| bedtools/2.18.0]]		* [[bedtools2.18 \| bedtools/2.18.0]]

← Older revision		Revision as of 16:42, 5 February 2015
Line 26:		Line 26:
	* [[allpathslg_48961 \| ALLPATHS-LG/48961]]		* [[allpathslg_48961 \| ALLPATHS-LG/48961]]
	* [[allpathslg 51910 \| ALLPATHS-LG/51910]]		* [[allpathslg 51910 \| ALLPATHS-LG/51910]]
			* [[ANGSD_0.614 \| angsd/0.614]]
	* [[augustus_2.7 \| augustus/2.7]]		* [[augustus_2.7 \| augustus/2.7]]
	* [[bedtools2.18 \| bedtools/2.18.0]]		* [[bedtools2.18 \| bedtools/2.18.0]]