Maker 2.2.8: Difference between revisions
| 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/ | /cm/shared/modulefiles/SHARED/ | ||
<source lang='tcl'> | <source lang='tcl'> | ||
| Line 18: | Line 18: | ||
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/ | 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/ | 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 | ||
Revision as of 10:01, 15 March 2014
Maker is a gene prediction/annotation pipeline.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
<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/SHARED/maker/maker-2.28/src/bin setenv TMPDIR /local
prepend-path PATH $maker_228_root 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
</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).