#### path to all the tools and references to run workflow


#### REFERENCES REQUIRED FOR LINCRNA WORKFLOW
BLAST_NR=@REFERENCE@/blast_db/nr
CHROMSIZE=@REFERENCE@/annotation/human/chromsize.txt
CHROMATIN_PEAK=@REFERENCE@/chromatin/human
CPAT_RDATA=@REFERENCE@/cpat/human/Human_train.RData
CPAT_HEXTAB=@REFERENCE@/cpat/human/Human_Hexamer.tab
EXON_BED=@REFERENCE@/annotation/human/genes_Illumina_iGenomes.mod.Exon.bed
FEATURES=@REFERENCE@/annotation/human/gencode.v12.annotation.gtf
GENE_MAPPING=@REFERENCE@/annotation/human/genes_Illumina_iGenomes.gene.mapping.txt
GENE_MAPPING_HG19=@REFERENCE@/annotation/human/genes_Illumina_iGenomes.gene.mapping.txt
GENCODE_BED=@REFERENCE@/annotation/human/Gencode.lincRNA.bed
K4_CHROMATIN=@REFERENCE@/chromatin/human/K4.merged.bed
K36_CHROMATIN=@REFERENCE@/chromatin/human/K36.merged.bed
MASK_FILE=@REFERENCE@/annotation/human/mask.fa
MIT_TRANSCRIPTS=@REFERENCE@/annotation/human/MIT_lincRNAs_transcripts.bed
PROTEIN_CODING=@REFERENCE@/annotation/human/Ensembl.UCSC.NCBI.gencode.protein_coding.hg19.bed
PFAM_DB_A=@REFERENCE@/pfam/human/Pfam-A.hmm
PFAM_DB_B=@REFERENCE@/pfam/human/Pfam-B.hmm
REF_GENOME=@REFERENCE@/hg19/37.1/allchr.fa
REF_GENOME_DIR=@REFERENCE@/hg19/37.1


#### TOOLS REQUIRED FOR LINCRNA WORKFLOW
BEDTOOLS=
BLASTC=
CUFFLINKS=
CPAT=
EMBOSS=
HMMSCAN=
HTSEQ=
JAVA=
PERL=
PICARD=
PYTHON=
R=
SGE=
SAMTOOLS=
SCRIPTURE=
WORKFLOW_PATH=@SOURCE@


#### env variable for lincRNA
HTSEQPATH=@HTSEQ@/lib/python2.7/site-packages
PYTHONPATH=/projects/bsi/bictools/apps/metadata/genomedata/arch/Linux-x86_64/lib/python2.7
PYTHON_CPAT=@CPAT@/lib/python2.7/site-packages


#### queue
CUFF_QUEUE=q.workflow
QUEUE=q.workflow


#### value for dashboard update can be yes/no
STANDALONE=Yes
DASHBOARD_UPDATE=No
NOTIFICATION_OPTION=a


#### Program parameters

#### ENV/PROGRAM PARAMETERS REQUIRED FOR LINCRNA WORKFLOW
BLAST_EVALUE=1e-4
CPAT_THRESHOLD=0.364
DOMAIN_INCLUSION_THRESHOLDS=10e-4
DOMAIN_REPORTING_THRESHOLDS=10e-4
MAX_FSA_SPLIT=100
MERGE_WINDOW=500
MIN_ORF_LENGTH=5
NEAREST_GENE_WINDOW=10000
EXTRACTNONPROTEIN=1
SPLITBAM=0
