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author siyuan
date Tue, 11 Mar 2014 12:14:01 -0400
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#PLEASE EDIT EACH VARIABLE BASED ON YOUR FILE SETTING!
#DON'T EDIT block title"--REF--", "--PBS--", "--BWA aln--", "--BWA samse--"
#Users may download REFERENCE files at http://bioinformatics.mdanderson.org/Software/PRADA/
#Set REFERENCE file paths according to your own settings. 

--REF--
compdb_fasta	=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.plus.genome.fasta
compdb_map		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.plus.genome.map
genome_fasta	=	/RIS/home/verhaakgroup/PRADA/hg19broad/Homo_sapiens_assembly19.fasta
genome_gtf		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Homo_sapiens.GRCh37.64.gtf
dbsnp_vcf		=	/RIS/home/verhaakgroup/PRADA/hg19broad/dbsnp_135.b37.vcf
select_tx		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.selected.transcripts
feature_file	=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.canonical.gene.exons.tab.txt
tx_seq_file		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.fasta
ref_anno		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.annotations
ref_map			=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.formatted.map
ref_fasta		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.formatted.fasta
cds_file		=	/RIS/home/verhaakgroup/PRADA/hg19broad/ensembl.hg19.cds.txt
txcat_file		=	/RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64_primary_transcript.txt

--PBS--
-M = szheng2@mdanderson.org
-q = long
-l = nodes=1:ppn=12,walltime=120:00:00		#nodes and ppn are required

--BWA aln--
-t = 12										#This should be equal to the number of ppn

--BWA samse--
-n = 100