Cegma 2.4: Difference between revisions
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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/ | /cm/shared/modulefiles/SHARED/ | ||
< | <pre> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## cegma 2.4 modulefile | ## cegma 2.4 modulefile | ||
| Line 18: | Line 18: | ||
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/ | setenv CEGMA /cm/shared/apps/SHARED/cegma/cegma_v2.4.010312/ | ||
set cegma_24_root /cm/shared/apps/ | set cegma_24_root /cm/shared/apps/SHARED/cegma_v2.4.010312/bin/ | ||
set cegma_24_perllib /cm/shared/apps/ | 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 | ||
prepend-path PERL5LIB $cegma_24_perllib | prepend-path PERL5LIB $cegma_24_perllib | ||
</ | </pre> | ||
== Installation details == | |||
Cegma was built from source, per the [http://korflab.ucdavis.edu/datasets/cegma/README installation instructions] provided. | |||
== See also == | == See also == | ||
* [[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] | ||
Latest revision as of 15:42, 15 June 2023
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
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
#%Module1.0#######################################################################
## cegma 2.4 modulefile
##
proc ModulesHelp { } {
puts stderr "\tAdds cegma 2.4 to your environment"
}
module-whatis "Adds cegma 2.4 to your environment"
module load BLAST+/2.2.28 genewise/2.2.3-rc7 geneid/1.4.4 hmmer/3.1b1
setenv CEGMA /cm/shared/apps/SHARED/cegma/cegma_v2.4.010312/
set cegma_24_root /cm/shared/apps/SHARED/cegma_v2.4.010312/bin/
set cegma_24_perllib /cm/shared/apps/SHARED/cegma/cegma_v2.4.010312/lib/
prepend-path PATH $cegma_24_root
prepend-path PERL5LIB $cegma_24_perllib
Installation details
Cegma was built from source, per the installation instructions provided.
See also
- Globally installed software
- ABGC specific modules
- BLAST+/2.2.28
- geneid/1.4.4
- genewise/2.2.3-rc7
- hmmer/3.1b1