ComputeVM: install_tools.sh

export PATH="/usr/share/lmod/lmod/libexec/:${PATH}"
export EASYBUILD_MODULES_TOOL=Lmod
PREFIX=$HOME/.local/easybuild
export EASYBUILD_INSTALLPATH="${PREFIX}"
module use /srv/molgenis/.local/easybuild/modules/base/
module load EasyBuild/2.0.0

echo "BEDTools"
eb EasyBuild/all/BEDTools-2.23.0-goolf-1.7.20.eb --robot

echo "BWA"
eb EasyBuild/all/BWA-0.7.12-goolf-1.7.20.eb --robot

echo "Java"
eb EasyBuild/all/Java-1.7.0_51.eb --robot

cp picard.py /srv/molgenis/.local/easybuild/software/EasyBuild/2.0.0/lib/python2.6/site-packages/easybuild_easyblocks-2.0.0-py2.6.egg/easybuild/easyblocks/p/picard.py

echo "Picard"
eb EasyBuild/all/picard-1.130.eb --robot

echo "BCFtools"
eb EasyBuild/all/BCFtools-1.2-goolf-1.7.20.eb --robot

echo "FastQC"
eb EasyBuild/all/FastQC-0.11.3-Java-1.7.0_76.eb --robot

echo "GATK"
eb EasyBuild/all/GATK-3.4-0-Java-1.7.0_51.eb --robot

echo "zlib"
eb EasyBuild/all/zlib-1.2.8-goolf-1.7.20.eb --robot

echo "libpng"
eb EasyBuild/all/libpng-1.6.16-goolf-1.7.20.eb --robot

echo "NASM"
eb EasyBuild/all/NASM-2.11.06-goolf-1.7.20.eb --robot

echo "libjpg"
eb EasyBuild/all/libjpeg-turbo-1.4.0-goolf-1.7.20.eb --robot

echo "libreadline"
eb EasyBuild/all/libreadline-6.3-goolf-1.7.20.eb --robot

echo "ncurses"
eb EasyBuild/all/ncurses-5.9-goolf-1.7.20.eb --robot

echo "Perl"
eb EasyBuild/all/Perl-5.20.2-goolf-1.7.20-bare.eb --robot

echo "R"
eb EasyBuild/all/R-3.1.2-goolf-1.7.20.eb --robot

echo "SNP"
eb EasyBuild/new/snpEff-v4.1d-Java-1.7.0_51.eb --robot

echo "tabix"
eb EasyBuild/new/tabix-0.2.6-goolf-1.7.20.eb --robot

echo ""
eb EasyBuild/newVCFtools-0.1.12b-goolf-1.7.20-Perl-5.20.2-bare.eb --robot