Maker 2.2.8: Difference between revisions
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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/ | /cm/shared/modulefiles/SHARED/ | ||
< | <pre> | ||
#%Module1.0####################################################################### | #%Module1.0####################################################################### | ||
## maker 2.28 modulefile | ## maker 2.28 modulefile | ||
| 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 | ||
</ | </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. | ||
== 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 == | ||
* [[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] | ||
Latest revision as of 15:43, 15 June 2023
Maker is a gene prediction/annotation pipeline.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
#%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
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).