Allpathslg 51910

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'>

1. %Module1.0#######################################################################
   1. 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.

See also

• Globally installed software
• ABGC specific modules

External links

• ALLPATHS-LG home page