# Created: Sat Oct 06 14:00:49 EDT 2012 by cgaadm_deadline
# Job: 180068    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:165
# Parameters: 
#    individual_set_id = GBM
#    mutation_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM/1780879/0.MutSigPreprocess.Finished/GBM.maf
#    coverage_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/GBM/1780922/0.ProcessCoverageForMutSig.Finished/GBM.coverage.mat
#    patient_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM/1780879/0.MutSigPreprocess.Finished/GBM.patients.txt
#    category_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/GBM/1780922/0.ProcessCoverageForMutSig.Finished/GBM.mutcategs.txt
#    gene_list = /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt
#    build = hg18
#    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/hg18/R.mat
#    build_dir = /xchip/cga1/annotation/db/ucsc/hg18
#    param_file = /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
#    mutation_preprocessing_report_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/GBM/1780879/0.MutSigPreprocess.Finished/GBM.mutation_preprocessing_report.txt
#    jobcount = 200
