Mercurial > repos > siyuan > prada
view pyPRADA_1.2/conf.txt @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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children | 03815b87eb65 |
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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=i2,walltime=120:00:00 #nodes and ppn are required --BWA aln-- -t = 2 #This should be equal to the number of ppn --BWA samse-- -n = 100