#### path to all the tools and references to run workflow
WORKFLOW=Circ-Seq
RUN_NAME=Test SGE version
EMAIL=nair.asha@mayo.edu
# Please provide path to aligned BAM files
BAM_DIR=/data2/bsi/staff_analysis/m069134/scripts/nair_asha_m069134/technologies/circRNA/Feb_2014/for_publication/test_sample
# Sample names should be colon seperated
SAMPLENAMES=test_sample
# Directory to which circRNA results will be written
CIRC_DIR=/data2/bsi/staff_analysis/m069134/scripts/nair_asha_m069134/technologies/circRNA/Feb_2014/for_publication/test_sample/circRNA
ANCHOR_SIZE=20
#--------------------------------------------------------------
#### references
REF_BOWTIE=/data2/bsi/reference/sequence/human/ncbi/37.1/indexed/allchr
REF_GENOME=/data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa
REF_GENOME_DIR=/data2/bsi/reference/sequence/human/ncbi/37.1/
BLAT_REF=/data2/bsi/reference/db/hg19.2bit

#### tools
BOWTIE=/projects/bsi/bictools/apps/alignment/bowtie/latest/
#PYTHON=/usr/local/biotools/python/2.7/bin
PYTHON=/home/m102324/bin/python2.7
SAMTOOLS=/projects/bsi/bictools/apps/alignment/samtools/0.1.18
SGE=/home/oge/ge2011.11/bin/linux-x64/
BEDTOOLS=/projects/bsi/bictools/apps/misc/BEDTools/2.16.2/bin/
BLAT=/projects/bsi/bictools/apps/alignment/blat/34_x64
WORKFLOW_PATH=/data2/bsi/staff_analysis/m069134/scripts/nair_asha_m069134/technologies/circRNA/Feb_2014/for_publication/SGE_version/

#### env variables
PYTHONPATH=/projects/bsi/bictools/apps/metadata/genomedata/arch/Linux-x86_64/lib/python2.7

#### queue
QUEUE=ngs-sec -l medp=TRUE

#### Queue parameters
NOTIFICATION_OPTION=ae
THREADS=8
