RepeatModeler 1.0.7: 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####################################################################### | ||
## RepeatModeler 1.0.7 modulefile | ## RepeatModeler 1.0.7 modulefile | ||
| Line 16: | Line 16: | ||
module-whatis "Adds RepeatModeler v1.0.7 to your environment" | module-whatis "Adds RepeatModeler v1.0.7 to your environment" | ||
set repeatmodeler_107_root /cm/shared/apps/ | set repeatmodeler_107_root /cm/shared/apps/SHARED/RepeatModeler/RepeatModeler-1-0-7/ | ||
prepend-path PATH $repeatmodeler_107_root | prepend-path PATH $repeatmodeler_107_root | ||
</ | </pre> | ||
== Installation details == | == Installation details == | ||
RepeatModeler requires several packages. | RepeatModeler requires several packages. | ||
* RepeatMasker; see the [[RepeatMasker_4.0.3 | relevant Wiki page]] | * RepeatMasker; see the [[RepeatMasker_4.0.3 | relevant Wiki page]] | ||
* RECON; RECON was compiled from source. Location: | * RECON; RECON was compiled from source. Location: | ||
/cm/shared/apps/ | /cm/shared/apps/SHARED/RECON/RECON-1.07 | ||
* RepeatScout; RepeatScout was compiled from source. Location: | * RepeatScout; RepeatScout was compiled from source. Location: | ||
/cm/shared/apps/ | /cm/shared/apps/SHARED/RepeatScout/RepeatScout-1 | ||
* rmblast; see the [[RepeatMasker_4.0.3 | RepeatMasker Wiki page]] | * rmblast; see the [[RepeatMasker_4.0.3 | RepeatMasker Wiki page]] | ||
* tandem repeat finder; see the [[RepeatMasker_4.0.3 | RepeatMasker Wiki page]] | * tandem repeat finder; see the [[RepeatMasker_4.0.3 | RepeatMasker Wiki page]] | ||
All dependencies are configured within RepeatModeler; Setting environment variables is therefore not required. | |||
== See also == | == See also == | ||
Latest revision as of 14:41, 15 June 2023
RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
#%Module1.0#######################################################################
## RepeatModeler 1.0.7 modulefile
##
proc ModulesHelp { } {
puts stderr "\tAdds RepeatModeler v1.0.7 to your environment"
}
module-whatis "Adds RepeatModeler v1.0.7 to your environment"
set repeatmodeler_107_root /cm/shared/apps/SHARED/RepeatModeler/RepeatModeler-1-0-7/
prepend-path PATH $repeatmodeler_107_root
Installation details
RepeatModeler requires several packages.
- RepeatMasker; see the relevant Wiki page
- RECON; RECON was compiled from source. Location:
/cm/shared/apps/SHARED/RECON/RECON-1.07
- RepeatScout; RepeatScout was compiled from source. Location:
/cm/shared/apps/SHARED/RepeatScout/RepeatScout-1
- rmblast; see the RepeatMasker Wiki page
- tandem repeat finder; see the RepeatMasker Wiki page
All dependencies are configured within RepeatModeler; Setting environment variables is therefore not required.