Installing software on marvin

Installing

Software needs to be installed in:

/usr/local/Modules/modulefiles/tools/<software name>/<version number>/

or

/shelf/modulefiles/

to make use of the modules feature. Beware using /usr/local/Modules/ as there's only 50Gb of space on /. Use /shelf/modulefiles/ for anything big (I'm looking at you interproscan).

The text files that tells modules that the software is there are located in:

/usr/local/Modules/3.2.10/modulefiles/<software>/<version number>

An example of which is below:

#%Module1.0#####################################################################
##
##
proc ModulesHelp { } {
        puts stderr "\tStacks - loads Stacks 2.0Beta7c software
\tSoftware available:
\tcstacks
\testacks
\thstacks
\tpstacks
\trxstacks
\tsstacks
\tustacks
"
} 

module-whatis	"loads Stacks version 1.41 software" 

module load perl samtools/0.1.19b sparsehash 

# for Tcl script use only
set	version		2.0Beta7c
set	prefix		/usr/local/Modules/modulefiles/tools/stacks/${version}
set     sys             linux64

setenv STACKSROOTDIR ${prefix}
prepend-path    PATH   		${prefix}/bin

Removing

Move the folder and it's associated module file into /shelf/scratch/root/dustbin_for_modules means we have it ready if we need to restore it.

Compiling

The non-standard location of the gcc binaries can cause problems. For configuring, use the line below to help:

 ./configure CXX=/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++  CPP='/usr/local/Modules/modulefiles/tools/gcc/4.9.3/bin/g++ -E' --prefix=whatever