modules

#!/bin/sh
## Script ready to be put on python virtualenv environment
## should be called from ~/.virtualenv/<workspace>/bin/postactivate
## *NOT* from .bashrc or 

# No python modules are loaded since only the ones
# in the virtual environment will be used.
# "mkvirtualenv --no-site-packages <workspace>" is assumed

MODS="bioinfo-tools
bowtie/0.12.7
samtools/0.1.12-10
bwa/0.6.2
maq/0.7.1
mosaik-aligner/1.0.1388
python/2.6.6
CASAVA/1.7.0
#picard/1.41
#GATK/1.4.21
cufflinks/2.0.2
tophat/1.3.3
Fastx/0.0.13
FastQC/0.7.2
R/2.14
emboss/6.4.0
gnuplot/4.4.3
BEDTools/2.11.2
freebayes"

# Custom modules from SciLifeLab/modules.sf.net
MODS="$MODS
fastqscreen/0.2.1
GATK/1.5
snpEff/2.0.5
picard/1.64
ucsc_tools/20120530"

#module purge

for mod in $MODS
do
	module load $mod >& /dev/null
done

# We unset PYTHONHOME set by the module system, 
# otherwise the system will not use the python
# of virtualenv
#unset PYTHONHOME
module unload python