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. | 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. | ||
== See also == | == See also == | ||
Revision as of 14:51, 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.