Maker 2.2.8: Difference between revisions
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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] | ||
Revision as of 22:33, 6 January 2014
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.
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).