# Created: Wed Oct 10 14:21:56 EDT 2012 by cgaadm_deadline
# Job: 181708    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:165
# Parameters: 
#    individual_set_id = BLCA
#    mutation_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.maf
#    coverage_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.coverage.mat
#    patient_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.patients.txt
#    category_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/BLCA/1685859/0.ProcessCoverageForMutSig.Finished/BLCA.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.params.txt
#    mutation_preprocessing_report_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/BLCA/1683137/0.MutSigPreprocess.Finished/BLCA.mutation_preprocessing_report.txt
#    jobcount = 200
