Allpathslg 51910: Difference between revisions
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Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly. | Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly. | ||
Testgenome derived from here and instructions followed in README: | |||
<source lang='bash'> | |||
wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz | |||
</source> | |||
== See also == | == See also == | ||
Revision as of 16:42, 4 February 2015
ALLPATHS-LG is a popular genome assembler.
Module file
The module file can be found in this location:
/cm/shared/modulefiles/SHARED/
<source lang='tcl'>
- %Module1.0#######################################################################
- maker ALLPATHS-LG (51910 modulefile
proc ModulesHelp { } {
puts stderr "\tAdds ALLPATHS-LG (51910) to your environment"
}
module-whatis "Adds ALLPATHS-LG (51910) to your environment"
module load gcc/4.8.1 setenv LC_ALL C
set allpathslg_51910_root /cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910/bin/
prepend-path PATH $allpathslg_51910_root
</source>
Installation details
ALLPATHS-LG 51910 was downloades as 'latest version':
<source lang='bash'> wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz </source>
It was compiled from source (using gcc4.8.1) on 03-02-2015:
<source lang='bash'> module load gcc/4.8.1 ./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910 make make install </source>
Available 200kbp testgenome initially failed to assemble. This was solved by setting 'LC_ALL=C'. This is handled by the module file and therefore does not require to be set in the local environment. With this tweak the test data set will run properly. Testgenome derived from here and instructions followed in README:
<source lang='bash'> wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/test.genome.tar.gz </source>