Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/conf.txt @ 0:acc2ca1a3ba4
Uploaded
| author | siyuan |
|---|---|
| date | Thu, 20 Feb 2014 00:44:58 -0500 |
| parents | |
| children | 03815b87eb65 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/conf.txt Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,31 @@ +#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 +