OMNI_VCF=/data2/bsi/reference/genetics/omni/hg19/1000G_omni2.5.hg19.sites.vcf
FUSION_MIN_DIST=50000
WORKFLOW_PATH=/projects/bsi/bictools/scripts/mrnaseq/MAPRSeq/tags/1.2.1.4
HTTP_SERVER=bmidev2
PICARD=/projects/bsi/bictools/apps/alignment/picard/1.67
REF_GENOME=/data2/bsi/reference/sequence/human/ncbi/hg19/indexed/allchr.fa
BOWTIE1=/projects/bsi/bictools/apps/alignment/bowtie/0.12.7
SGE=/home/oge/ge2011.11/bin/linux-x64
GENE_MAPPING=/data2/external_data/Bockol_Matthew_m084061/maprseq/sample_output/maprseq/mrnaseq/test_sample/genes_Illumina_iGenomes.gene.mapping.txt
REF_FLAT=/data2/bsi/reference/tophat/hg19.refflat
DASHBOARD_JAR=/home/m082166/AddSecTest
DBSNP_REF=/data2/bsi/reference/annotation/dbSNP/hg19/dbsnp_135.hg19.vcf.gz
KARYOTYPE=/data2/bsi/reference/tophat/karyotype.human.hg19.txt
CHROMSIZE=/data2/bsi/reference/tophat/chromsize.txt
NT_BLAST_DB=/data5/bsi/refdata/blast_db/latest/nt
PYTHONPATH=/projects/bsi/bictools/apps/metadata/genomedata/arch/Linux-x86_64/lib/python2.7
MATE_SD=33
REF_GENE_BED=/data5/bsi/refdata/BOWTIE/hg19_refGene_table.bed
HAPMAP_VCF=/data2/bsi/reference/genetics/hapmap/hg19/hapmap_3.3.hg19.sites.vcf
REF_BOWTIE=/data2/bsi/reference/sequence/human/ncbi/hg19/indexed/allchr
TABIX=/projects/bsi/bictools/apps/alignment/tabix/0.2.5
INSERT_SIZE=107
STANDALONE=NO
QUEUE=ngs-sec -l medp~TRUE
NOTIFICATION_OPTION=a
REFGENE=/data2/bsi/reference/tophat/refGene.txt
FUSION=
ENSGENE=/data2/bsi/reference/tophat/ensGene.txt
R=/usr/local/biotools/r/R-2.14.0/bin
TOPHAT=/projects/bsi/bictools/apps/alignment/tophat/2.0.6
EXON_BED=/data2/external_data/Bockol_Matthew_m084061/maprseq/sample_output/maprseq/mrnaseq/test_sample/genes_Illumina_iGenomes.exon.bed
MCL=/data2/bsi/reference/tophat/mcl
MAX_HITS=20
HTSEQPATH=/projects/bsi/bictools/apps/mrnaseq/htseq/0.5.3p9/lib/python2.7/site-packages
BLAT_REF=/data2/bsi/reference/db/hg19.2bit
BLASTC=/usr/local/biotools/blast/ncbi-blast-2.2.23+/bin
STD_PERL5LIB=/usr/local/biotools/perl/5.10.0/lib
MASTER_GENE_FILE=/data2/bsi/reference/misc/hg19.master.gene.bed
HG_BLAST_DB=/data5/bsi/refdata/blast_db/latest/human_genomic
CIRCOS=/projects/bsi/bictools/apps/visualizers/circos/circos-0.54/bin
PYTHON=/usr/local/biotools/python/2.7/bin
FEATURES=/data2/external_data/Bockol_Matthew_m084061/maprseq/sample_output/maprseq/mrnaseq/test_sample/genes_Illumina_iGenomes.mod.gtf
UCSC_BIN=/projects/bsi/bictools/apps/visualizers/jksrc/bin/x86_64
GATK_QUEUE=ngs-sec -l medp~TRUE
JAVA=/usr/local/biotools/java/jre1.6.0_20/bin
GATK=/projects/bsi/bictools/apps/alignment/GenomeAnalysisTK/1.7
HTSEQ=/projects/bsi/bictools/apps/mrnaseq/htseq/0.5.3p9
PERL=/usr/local/biotools/perl/5.14.2/bin/perl
TRANSCRIPTOME_HG19_INDEX=/data2/bsi/reference/tophat/transcriptome/hg19/index
SEGMENT_SIZE=25
FASTQC=/projects/bsi/bictools/apps/qc/FastQC
RSEQCPATH=/projects/bsi/bictools/apps/mrnaseq/rseqc/latest/usr/local/biotools/python/2.7/lib/python2.7/site-packages
BOWTIE=/projects/bsi/bictools/apps/alignment/bowtie/2.0.2
RSEQC=/projects/bsi/bictools/apps/mrnaseq/rseqc/2.3.2/usr/local/biotools/python/2.7/bin
DASHBOARD_UPDATE=YES
BEDTOOLS=/projects/bsi/bictools/apps/misc/BEDTools/2.16.2/bin
SAMTOOLS=/projects/bsi/bictools/apps/alignment/samtools/0.1.18
BLAT=/projects/bsi/bictools/apps/alignment/blat/34_x64
