Maker 2.2.8: Difference between revisions
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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] | ||
Revision as of 11:45, 21 December 2013
Maker is a gene prediction/annotation pipeline.
Module file
The module file can be found in this location:
/cm/shared/apps/WUR/ABGC/modulefiles
<source lang='tcl'>
- %Module1.0#######################################################################
- maker 2.28 modulefile
proc ModulesHelp { } {
puts stderr "\tAdds 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
set maker_228_root /cm/shared/apps/WUR/ABGC/maker/maker-2.28/src/bin setenv TMPDIR /local
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
prepend-path PERL5LIB $maker_228_perllib
</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.