RepeatMasker 4.0.3: Difference between revisions
(Created page with "[http://www.repeatmasker.org RepeatMasker]RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the pro...") |
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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/ | ||
<source lang='tcl'> | <source lang='tcl'> | ||
| Line 16: | Line 16: | ||
module-whatis "Adds RepeatMasker v4.0.3 to your environment" | module-whatis "Adds RepeatMasker v4.0.3 to your environment" | ||
set repeatmasker_403_root /cm/shared/apps/ | set repeatmasker_403_root /cm/shared/apps/SHARED/RepeatMasker/RepeatMasker-4-0-3/ | ||
prepend-path PATH $repeatmasker_403_root | prepend-path PATH $repeatmasker_403_root | ||
| Line 22: | Line 22: | ||
</source> | </source> | ||
Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the <code>TMPDIR</code> environment variable gets set to <code>/local</code>. Also note that Maker requires an Sqlite database. Sqlite databases are (currently) not compatible with the Lustre file system. | Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the <code>TMPDIR</code> environment variable gets set to <code>/local</code>. Also note that Maker requires an Sqlite database. Sqlite databases are (currently) not compatible with the Lustre file system. | ||
== Installation details == | |||
Pre-compiled rmblast (NCBI BLAST+ optimized for RepeatMasker) downloaded from the [http://www.repeatmasker.org/RMBlast.html RepeatMasker download pages]. Location of rmblast: | |||
/cm/shared/apps/SHARED/blast/rmblast-2.2.28 | |||
The default search engine is 'ncbi' (rmblast). Alternative search engines are possible. Currently, only hmmer 3.1 is installed as alternative search engine. | |||
Pre-compile binary of [http://tandem.bu.edu/trf/trf.html Tandem Repeat Finder] (TRF,trf) v4.0.4 were downloaded from the TRF homepage and can be found: | |||
/cm/shared/apps/SHARED/tandem_repeat_finder/trf404.linux64 | |||
The soft links 'TRF' and 'trf' can be found in the same folder. Some programs (e.g. RepeatModeler) may require this as default binary name. | |||
Installed [http://www.girinst.org RepBase] libraries include the 2013-04-22 RepeatMasker version. Dfam 1.2 is provided as default in the RepeatMasker package. | |||
/cm/shared/apps/SHARED/RepeatMasker/RepeatMasker-4-0-3/Libraries | |||
== See also == | == See also == | ||
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== External links == | == External links == | ||
* [http://www. | * [http://www.repeatmasker.org RepeatMasker homepage] | ||
* [http:// | * [http://www.girinst.org RepBase homepage] | ||
Latest revision as of 10:11, 15 March 2014
RepeatMaskerRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (i.e. replaced by Ns or put to lowercase). RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
<source lang='tcl'>
- %Module1.0#######################################################################
- RepeatMasker 4.0.3 modulefile
proc ModulesHelp { } {
puts stderr "\tAdds RepeatMasker v4.0.3 to your environment"
}
module-whatis "Adds RepeatMasker v4.0.3 to your environment"
set repeatmasker_403_root /cm/shared/apps/SHARED/RepeatMasker/RepeatMasker-4-0-3/
prepend-path PATH $repeatmasker_403_root
</source>
Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the TMPDIR environment variable gets set to /local. Also note that Maker requires an Sqlite database. Sqlite databases are (currently) not compatible with the Lustre file system.
Installation details
Pre-compiled rmblast (NCBI BLAST+ optimized for RepeatMasker) downloaded from the RepeatMasker download pages. Location of rmblast:
/cm/shared/apps/SHARED/blast/rmblast-2.2.28
The default search engine is 'ncbi' (rmblast). Alternative search engines are possible. Currently, only hmmer 3.1 is installed as alternative search engine.
Pre-compile binary of Tandem Repeat Finder (TRF,trf) v4.0.4 were downloaded from the TRF homepage and can be found:
/cm/shared/apps/SHARED/tandem_repeat_finder/trf404.linux64
The soft links 'TRF' and 'trf' can be found in the same folder. Some programs (e.g. RepeatModeler) may require this as default binary name.
Installed RepBase libraries include the 2013-04-22 RepeatMasker version. Dfam 1.2 is provided as default in the RepeatMasker package.
/cm/shared/apps/SHARED/RepeatMasker/RepeatMasker-4-0-3/Libraries