example.env

## Get your hostname by `hostname -f`

[your_hostname]

mod_chipseq = bwa/0.7.7 samtools/0.1.19 bedtools/2.19.1 ucsc_tools/3.0.9 picard-tools/1.92 MACS2/2.1.0 java/latest

addpath_chipseq = /srv/gsfs0/scratch/leepc12/software/idrCode:/srv/gsfs0/scratch/leepc12/software/phantompeakqualtools:/srv/gsfs0/scratch/leepc12/software/idr/bin:/srv/gsfs0/scratch/leepc12/software/align2rawsignal/bin:/srv/gsfs0/scratch/leepc12/software/gem:/srv/gsfs0/scratch/leepc12/software/deepTools/bin:/srv/gsfs0/scratch/leepc12/software/R-2.15.1/bin:/srv/gsfs0/scratch/leepc12/software/python3.4/bin:/srv/gsfs0/scratch/leepc12/software/python2.7/bin

shcmd_chipseq = export GEMROOT=/srv/gsfs0/scratch/leepc12/software/gem; export GEM=/srv/gsfs0/scratch/leepc12/software/gem/gem.jar; export LAPACK=/srv/gsfs0/scratch/leepc12/software/blas/lapack-*/liblapack.a; export _JAVA_OPTIONS='-Xms256M -Xmx512M -XX:ParallelGCThreads=1'; export MAX_JAVA_MEM='8G'; export MALLOC_ARENA_MAX=4; MCRROOT=/srv/gsfs0/scratch/leepc12/software/MATLAB_Compiler_Runtime/v714; LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/runtime/glnxa64; LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64; MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64; LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads; LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server; LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}; XAPPLRESDIR=${MCRROOT}/X11/app-defaults; export LD_LIBRARY_PATH; export XAPPLRESDIR;

species_file = $script_dir/species/scg3.conf

use_sys_default = true	# unlimited resource