# Created: Fri Nov 16 04:45:41 EST 2012 by cgaadm
# Job: 238745    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:170
# Parameters: 
#    individual_set_id = THCA
#    mutation_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.maf
#    coverage_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/THCA/1911864/0.ProcessCoverageForMutSig.Finished/THCA.coverage.mat
#    patient_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.patients.txt
#    category_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/THCA/1911864/0.ProcessCoverageForMutSig.Finished/THCA.mutcategs.txt
#    gene_list = /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt
#    build = hg19
#    geneset_file = /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt
#    cosmic_file = /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv
#    refseq_file = /xchip/cga1/annotation/db/ucsc/hg19/R.mat
#    build_dir = /xchip/cga1/annotation/db/ucsc/hg19
#    param_file = /xchip/cga1/reference/mutsig_params/MutSig2.0_cga.pancan.blacklist.v7.hg19.params.txt
#    mutation_preprocessing_report_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/THCA/1911605/0.MutSigPreprocess.Finished/THCA.mutation_preprocessing_report.txt
#    jobcount = 200
