RepeatModeler 1.0.7
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/
<source lang='tcl'>
- %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
</source>
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.