Allpathslg 51910

ALLPATHS-LG is a popular genome assembler.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

#%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

Installation details

ALLPATHS-LG 51910 was downloades as 'latest version':

wget ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz

It was compiled from source (using gcc4.8.1) on 03-02-2015:

module load gcc/4.8.1
./configure --prefix=/cm/shared/apps/SHARED/ALLPATHS-LG/allpathslg-51910
make
make install

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