Cegma 2.4 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T14:42:25Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:42, 15 June 2023
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	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## cegma 2.4 modulefile		## cegma 2.4 modulefile
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	prepend-path PERL5LIB $cegma_24_perllib		prepend-path PERL5LIB $cegma_24_perllib

	</~~source~~>		</pre>

	== Installation details ==		== Installation details ==

Megen002: /* Module file */

2014-03-15T08:58:43Z

Module file

← Older revision		Revision as of 10:58, 15 March 2014
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	== Module file ==		== Module file ==
	The module file can be found in this location:		The module file can be found in this location:
	/cm/shared/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/cm/shared/modulefiles/SHARED/

	<source lang='tcl'>		<source lang='tcl'>
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	module load BLAST+/2.2.28 genewise/2.2.3-rc7 geneid/1.4.4 hmmer/3.1b1		module load BLAST+/2.2.28 genewise/2.2.3-rc7 geneid/1.4.4 hmmer/3.1b1

	setenv CEGMA /cm/shared/apps/~~WUR/ABGC~~/cegma/cegma_v2.4.010312/		setenv CEGMA /cm/shared/apps/SHARED/cegma/cegma_v2.4.010312/

	set cegma_24_root /cm/shared/apps/~~WUR/ABGC/cegma~~/cegma_v2.4.010312/bin/		set cegma_24_root /cm/shared/apps/SHARED/cegma_v2.4.010312/bin/
	set cegma_24_perllib /cm/shared/apps/~~WUR/ABGC~~/cegma/cegma_v2.4.010312/lib/		set cegma_24_perllib /cm/shared/apps/SHARED/cegma/cegma_v2.4.010312/lib/

	prepend-path PATH $cegma_24_root		prepend-path PATH $cegma_24_root

Megen002 at 13:19, 21 December 2013

2013-12-21T13:19:46Z

← Older revision		Revision as of 15:19, 21 December 2013
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	</source>		</source>

			== Installation details ==
			Cegma was built from source, per the [http://korflab.ucdavis.edu/datasets/cegma/README installation instructions] provided.

	== See also ==		== See also ==

Megen002: /* See also */

2013-12-21T12:13:27Z

Megen002 at 12:11, 21 December 2013

2013-12-21T12:11:43Z

← Older revision		Revision as of 14:11, 21 December 2013
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			CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. The strategy relies on a simple fact: some highly conserved proteins are encoded in essentially all eukaryotic genomes.

	== Module file ==		== Module file ==
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	== External links ==		== External links ==
	* [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA homepage at Korf Lab]		* [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA homepage at Korf Lab]
			* [http://korflab.ucdavis.edu/Datasets/cegma/README CEGMA README]

Megen002 at 12:02, 21 December 2013

2013-12-21T12:02:22Z

← Older revision		Revision as of 14:02, 21 December 2013
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	<source lang='tcl'>		<source lang='tcl'>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## ~~bwa 0~~.~~7.5a~~ modulefile		## cegma 2.4 modulefile
	##		##
	proc ModulesHelp { } {		proc ModulesHelp { } {

	puts stderr "\tAdds ~~bwa v0~~.~~7.5a~~ to your environment"		puts stderr "\tAdds cegma 2.4 to your environment"
	}		}

	module-whatis "Adds ~~bwa v0~~.~~7.5a~~ to your environment"		module-whatis "Adds cegma 2.4 to your environment"

	~~set bwa_075a_root~~ /cm/~~shared~~/~~apps/WUR/ABGC/bwa~~/~~bwa-0.7~~.5a		module load BLAST+/2.2.28 genewise/2.2.3-rc7 geneid/1.4.4 hmmer/3.1b1

	~~prepend-path PATH $bwa_075a_root~~		setenv CEGMA /cm/shared/apps/WUR/ABGC/cegma/cegma_v2.4.010312/

			set cegma_24_root /cm/shared/apps/WUR/ABGC/cegma/cegma_v2.4.010312/bin/
			set cegma_24_perllib /cm/shared/apps/WUR/ABGC/cegma/cegma_v2.4.010312/lib/

			prepend-path PATH $cegma_24_root
			prepend-path PERL5LIB $cegma_24_perllib

	</source>		</source>
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	== External links ==		== External links ==
	* [http://~~bio-bwa~~.~~sourceforge~~.~~net~~/~~bwa.shtml BWA manpage~~]		* [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA homepage at Korf Lab]

Megen002: Created page with " == Module file == The module file can be found in this location: /cm/shared/apps/WUR/ABGC/modulefiles #%Module1.0######################################..."

2013-12-21T11:52:05Z

Created page with " == Module file == The module file can be found in this location: /cm/shared/apps/WUR/ABGC/modulefiles <source lang='tcl'> #%Module1.0######################################..."

New page

== Module file ==
The module file can be found in this location:
/cm/shared/apps/WUR/ABGC/modulefiles

<source lang='tcl'>
#%Module1.0#######################################################################
## bwa 0.7.5a modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds bwa v0.7.5a to your environment"
}

module-whatis "Adds bwa v0.7.5a to your environment"

set bwa_075a_root /cm/shared/apps/WUR/ABGC/bwa/bwa-0.7.5a

prepend-path PATH $bwa_075a_root

</source>

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://bio-bwa.sourceforge.net/bwa.shtml BWA manpage]

← Older revision		Revision as of 14:13, 21 December 2013
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	* [[Globally_installed_software \| Globally installed software]]		* [[Globally_installed_software \| Globally installed software]]
	* [[ABGC_modules \| ABGC specific modules]]		* [[ABGC_modules \| ABGC specific modules]]
			* [[BLAST \| BLAST+/2.2.28]]
			* [[geneid_1.4.4 \| geneid/1.4.4]]
			* [[genewise_2.2.3 \| genewise/2.2.3-rc7]]
			* [[hmmer_3.1 \| hmmer/3.1b1]]

	== External links ==		== External links ==
	* [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA homepage at Korf Lab]		* [http://korflab.ucdavis.edu/Datasets/cegma/ CEGMA homepage at Korf Lab]
	* [http://korflab.ucdavis.edu/Datasets/cegma/README CEGMA README]		* [http://korflab.ucdavis.edu/Datasets/cegma/README CEGMA README]