Maker 2.2.8 - Revision history

Prins0891: to

 to fix code blocks

2023-06-15T14:43:42Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:43, 15 June 2023
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	/cm/shared/modulefiles/SHARED/		/cm/shared/modulefiles/SHARED/

	<~~source lang='tcl'~~>		<pre>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## maker 2.28 modulefile		## maker 2.28 modulefile
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	prepend-path PERL5LIB $maker_228_perllib		prepend-path PERL5LIB $maker_228_perllib

	</~~source~~>		</pre>
	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.

Megen002: /* Module file */

2014-03-15T09:01:28Z

Module file

← Older revision		Revision as of 11:01, 15 March 2014
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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/~~apps~~/~~WUR~~/~~ABGC/modulefiles~~		/cm/shared/modulefiles/SHARED/

	<source lang='tcl'>		<source lang='tcl'>
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	module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29 augustus/2.7		module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29 augustus/2.7

	set maker_228_root /cm/shared/apps/~~WUR/ABGC~~/maker/maker-2.28/src/bin		set maker_228_root /cm/shared/apps/SHARED/maker/maker-2.28/src/bin
	setenv TMPDIR /local		setenv TMPDIR /local

	prepend-path PATH $maker_228_root		prepend-path PATH $maker_228_root
	set maker_228_perllib /cm/shared/apps/~~WUR/ABGC~~/maker/maker-2.28/perl/lib:/cm/shared/apps/~~WUR/ABGC~~/maker/maker-2.28/lib		set maker_228_perllib /cm/shared/apps/SHARED/maker/maker-2.28/perl/lib:/cm/shared/apps/SHARED/maker/maker-2.28/lib

	prepend-path PERL5LIB $maker_228_perllib		prepend-path PERL5LIB $maker_228_perllib

2014-01-06T21:33:04Z

2013-12-21T12:09:31Z

← Older revision		Revision as of 14:09, 21 December 2013
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	</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 ==
			Built from source. Perl dependencies, including BioPerl resolved by 'Build resolvedeps' function. Version of default BioPerl installed on the cluster was not compatible with Maker requirements (too old).

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

2013-12-21T10:45:19Z

2013-12-21T10:30:07Z

Module file

← Older revision		Revision as of 12:30, 21 December 2013
Line 27:		Line 27:

	</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>.		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 ==		== See also ==

2013-12-21T00:36:34Z

← Older revision		Revision as of 02:36, 21 December 2013
Line 16:		Line 16:
	module-whatis "Adds maker 2.28 to your environment"		module-whatis "Adds maker 2.28 to your environment"

	module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29		module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29 augustus/2.7

	set maker_228_root /cm/shared/apps/WUR/ABGC/maker/maker-2.28/src/bin		set maker_228_root /cm/shared/apps/WUR/ABGC/maker/maker-2.28/src/bin

2013-12-20T20:27:53Z

← Older revision		Revision as of 22:27, 20 December 2013
Line 27:		Line 27:

	</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>.
	== See also ==		== See also ==

2013-12-20T20:25:44Z

← Older revision		Revision as of 22:25, 20 December 2013
Line 16:		Line 16:
	module-whatis "Adds maker 2.28 to your environment"		module-whatis "Adds maker 2.28 to your environment"

	module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29 ~~augustus/2.7~~		module load BLAST+/2.2.28 RepeatMasker/4.0.3 exonerate/2.2.0-x86_64 snap/2013-11-29

	set maker_228_root /cm/shared/apps/WUR/ABGC/maker/maker-2.28/src/bin		set maker_228_root /cm/shared/apps/WUR/ABGC/maker/maker-2.28/src/bin
			setenv TMPDIR /local

	prepend-path PATH $maker_228_root		prepend-path PATH $maker_228_root
Line 24:		Line 25:

	prepend-path PERL5LIB $maker_228_perllib		prepend-path PERL5LIB $maker_228_perllib

	</source>		</source>

2013-12-20T20:12:18Z

← Older revision		Revision as of 22:12, 20 December 2013
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	Maker is gene prediction/annotation pipeline.		Maker is a gene prediction/annotation pipeline.

	== Module file ==		== Module file ==

← Older revision		Revision as of 23:33, 6 January 2014
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	* [[Globally_installed_software \| Globally installed software]]		* [[Globally_installed_software \| Globally installed software]]
	* [[ABGC_modules \| ABGC specific modules]]		* [[ABGC_modules \| ABGC specific modules]]
			* [[Maker_protocols_Pmajor \| Maker protocols for ''Parus major'' genome]]

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

← Older revision		Revision as of 12:45, 21 December 2013
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	== See also ==		== See also ==
			* [[Globally_installed_software \| Globally installed software]]
			* [[ABGC_modules \| ABGC specific modules]]

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