RepeatModeler 1.0.7: Difference between revisions
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[http://www.repeatmasker.org/RepeatModeler.html 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 == | == 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 | ||
## | ## | ||
proc ModulesHelp { } { | proc ModulesHelp { } { | ||
puts stderr "\tAdds | puts stderr "\tAdds RepeatModeler v1.0.7 to your environment" | ||
} | } | ||
module-whatis "Adds | module-whatis "Adds RepeatModeler v1.0.7 to your environment" | ||
set | set repeatmodeler_107_root /cm/shared/apps/SHARED/RepeatModeler/RepeatModeler-1-0-7/ | ||
prepend-path PATH $ | prepend-path PATH $repeatmodeler_107_root | ||
</pre> | |||
== Installation details == | |||
RepeatModeler requires several packages. | |||
* RepeatMasker; see the [[RepeatMasker_4.0.3 | 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_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 == | ||
| Line 28: | Line 38: | ||
== External links == | == External links == | ||
* [http:// | * [http://www.repeatmasker.org/RepeatModeler.html RepeatModeler page] | ||
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.