#### path to all the tools and references to run workflow
WORKFLOW=Circ-Seq
# Please provide run name
RUN_NAME=Example run
EMAIL=user.name@institution.edu
# Please provide path to aligned BAM files
BAM_DIR=/path/to/unmapped/BAMfile/directory/
# Sample names should be colon seperated
SAMPLENAMES=test_sample
# Directory to which circRNA results will be written
CIRC_DIR=/path/to/output/circRNA/directory/
ANCHOR_SIZE=20
#--------------------------------------------------------------
#### references
REF_BOWTIE=/path/to/hg19
REF_GENOME=/path/to/hg19.fa
REF_GENOME_DIR=/path/to/directory/containing/hg19.fa/
BLAT_REF=/path/to/hg19.2bit
EXON_START_BOUNDARY=/path/to/exon_start_boundary.bed
EXON_END_BOUNDARY=/path/to/exon_end_boundary.bed
INTRON_START_BOUNDARY=/path/to/intron_start_boundary.bed
INTRON_END_BOUNDARY=/path/to/intron_end_boundary.bed
EXONS=/path/to/exons.bed

#### tools
BOWTIE=/path/to/bowtie 2.1.0/
PYTHON=/path/to/python/2.7/bin
SAMTOOLS=/path/to/samtools/0.1.18
SGE=/path/to/oge/ge2011.11/bin/linux-x64/
BEDTOOLS=/path/to/BEDTools/2.16.2/bin/
BLAT=/path/to/blat/34_x64
WORKFLOW_PATH=/path/to/where/Circ-Seq/scripts/are/located/

#### env variables
PYTHONPATH=/path/to/Linux-x86_64/lib/python2.7
