RepeatMasker 4.0.3 - Revision history

Megen002: /* Installation details */

2014-03-15T09:11:16Z

Installation details

← Older revision		Revision as of 11:11, 15 March 2014
Line 25:		Line 25:
	== Installation details ==		== 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:		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/~~WUR/ABGC~~/blast/rmblast-2.2.28		/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.		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:		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/~~WUR/ABGC~~/tandem_repeat_finder/trf404.linux64		/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.		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.		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/~~WUR/ABGC~~/RepeatMasker/RepeatMasker-4-0-3/Libraries		/cm/shared/apps/SHARED/RepeatMasker/RepeatMasker-4-0-3/Libraries

	== See also ==		== See also ==

Megen002: /* Module file */

2014-03-15T09:10:36Z

Module file

← Older revision		Revision as of 11:10, 15 March 2014
Line 3:		Line 3:
	== Module file ==		== Module file ==
	The module file can be found in this location:		The module file can be found in this location:
	/cm/shared/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/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/~~WUR/ABGC~~/RepeatMasker/RepeatMasker-4-0-3/		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

Megen002: /* Installation details */

2013-12-21T12:32:29Z

Installation details

← Older revision		Revision as of 14:32, 21 December 2013
Line 27:		Line 27:
	/cm/shared/apps/WUR/ABGC/blast/rmblast-2.2.28		/cm/shared/apps/WUR/ABGC/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.		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:		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/WUR/ABGC/tandem_repeat_finder/trf404.linux64		/cm/shared/apps/WUR/ABGC/tandem_repeat_finder/trf404.linux64

Megen002: /* Installation details */

2013-12-21T12:32:15Z

Installation details

← Older revision		Revision as of 14:32, 21 December 2013
Line 27:		Line 27:
	/cm/shared/apps/WUR/ABGC/blast/rmblast-2.2.28		/cm/shared/apps/WUR/ABGC/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.		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:		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/WUR/ABGC/tandem_repeat_finder/trf404.linux64		/cm/shared/apps/WUR/ABGC/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.		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.		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/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/Libraries		/cm/shared/apps/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/Libraries

Megen002: /* Installation details */

2013-12-21T12:30:56Z

Installation details

← Older revision		Revision as of 14:30, 21 December 2013
Line 27:		Line 27:
	/cm/shared/apps/WUR/ABGC/blast/rmblast-2.2.28		/cm/shared/apps/WUR/ABGC/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.		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) were downloaded from the TRF homepage and can be found:		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/WUR/ABGC/tandem_repeat_finder		/cm/shared/apps/WUR/ABGC/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.		Installed RepBase libraries include the 2013-04-22 RepeatMasker version. Dfam 1.2 is provided as default in the RepeatMasker package.

Megen002: /* Installation details */

2013-12-21T12:29:14Z

Installation details

← Older revision		Revision as of 14:29, 21 December 2013
Line 29:		Line 29:
	Pre-compile binary of Tandem Repeat Finder (TRF,trf) were downloaded from the TRF homepage and can be found:		Pre-compile binary of Tandem Repeat Finder (TRF,trf) were downloaded from the TRF homepage and can be found:
	/cm/shared/apps/WUR/ABGC/tandem_repeat_finder		/cm/shared/apps/WUR/ABGC/tandem_repeat_finder

			Installed RepBase libraries include the 2013-04-22 RepeatMasker version. Dfam 1.2 is provided as default in the RepeatMasker package.
			/cm/shared/apps/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/Libraries

	== See also ==		== See also ==

Megen002: /* Installation details */

2013-12-21T12:26:23Z

Installation details

← Older revision		Revision as of 14:26, 21 December 2013
Line 26:		Line 26:
	Pre-compiled rmblast (NCBI BLAST+ optimized for RepeatMasker) downloaded from the [http://www.repeatmasker.org/RMBlast.html RepeatMasker download pages]. Location of rmblast:		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/WUR/ABGC/blast/rmblast-2.2.28		/cm/shared/apps/WUR/ABGC/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) were downloaded from the TRF homepage and can be found:
			/cm/shared/apps/WUR/ABGC/tandem_repeat_finder

	== See also ==		== See also ==

Megen002 at 12:22, 21 December 2013

2013-12-21T12:22:26Z

← Older revision		Revision as of 14:22, 21 December 2013
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/WUR/ABGC/blast/rmblast-2.2.28

	== See also ==		== See also ==

Megen002: /* External links */

2013-12-21T10:51:47Z

External links

← Older revision		Revision as of 12:51, 21 December 2013
Line 28:		Line 28:

	== External links ==		== External links ==
	* [http://www.~~yandell-lab~~.org~~/software/maker.html Maker~~ homepage]		* [http://www.repeatmasker.org RepeatMasker homepage]
	* [http://~~gmod~~.org~~/wiki/MAKER_Tutorial_2013 Maker tutorial~~]		* [http://www.girinst.org RepBase homepage]

Megen002: 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..."

2013-12-21T10:50:39Z

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..."

New page

[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 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/apps/WUR/ABGC/modulefiles

<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/WUR/ABGC/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 <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.

== See also ==
* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

== External links ==
* [http://www.yandell-lab.org/software/maker.html Maker homepage]
* [http://gmod.org/wiki/MAKER_Tutorial_2013 Maker tutorial]