speedseq.config

#!/bin/bash -e

# general
SPEEDSEQ_HOME=/gscmnt/gc2719/halllab/src/speedseq
SAMBAMBA=$SPEEDSEQ_HOME/bin/sambamba
BGZIP=$SPEEDSEQ_HOME/bin/bgzip
TABIX=$SPEEDSEQ_HOME/bin/tabix
VAWK=$SPEEDSEQ_HOME/bin/vawk
PARALLEL=$SPEEDSEQ_HOME/bin/parallel
PYTHON=`which python2.7 || true` # python 2.7 must have numpy, scipy, and pysam installed

# align
BWA=$SPEEDSEQ_HOME/bin/bwa
SAMBLASTER=$SPEEDSEQ_HOME/bin/samblaster

# var/somatic
FREEBAYES=$SPEEDSEQ_HOME/bin/freebayes
VEP=$SPEEDSEQ_HOME/bin/variant_effect_predictor.pl
VEP_CACHE_DIR=$SPEEDSEQ_HOME/annotations/vep_cache

# sv
LUMPYEXPRESS=$SPEEDSEQ_HOME/bin/lumpyexpress
LUMPY=$SPEEDSEQ_HOME/bin/lumpy
PAIREND_DISTRO=$SPEEDSEQ_HOME/bin/pairend_distro.py
SVTYPER=$SPEEDSEQ_HOME/bin/svtyper
BAMGROUPREADS=$SPEEDSEQ_HOME/bin/bamgroupreads.py
BAMFILTERRG=$SPEEDSEQ_HOME/bin/bamfilterrg.py
BAMLIBS=$SPEEDSEQ_HOME/bin/bamlibs.py

# CNVnator
source /gsc/pkg/root/root/bin/thisroot.sh
CNVNATOR_WRAPPER=$SPEEDSEQ_HOME/bin/cnvnator_wrapper.py
CNVNATOR=$SPEEDSEQ_HOME/bin/cnvnator
ANNOTATE_RD=$SPEEDSEQ_HOME/bin/annotate_rd.py
CNVNATOR_CHROMS_DIR=$SPEEDSEQ_HOME/annotations/cnvnator_chroms

# re-align
BAMTOFASTQ=$SPEEDSEQ_HOME/bin/bamtofastq.py
MBUFFER=$SPEEDSEQ_HOME/bin/mbuffer
BAMHEADRG=$SPEEDSEQ_HOME/bin/bamheadrg.py
BAMCLEANHEADER=$SPEEDSEQ_HOME/bin/bamcleanheader.py