Maker 2.2.8: Difference between revisions

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Maker is gene prediction/annotation pipeline.
Maker is a gene prediction/annotation pipeline.


== 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'>
<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/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


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
</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.
 
== 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]]
* [[ABGC_modules | ABGC specific modules]]
* [[Maker_protocols_Pmajor | Maker protocols for ''Parus major'' genome]]


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

See also

External links