# Created: Thu Oct 25 01:36:13 EDT 2012 by cgaadm_deadline
# Job: 215313    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:170
# Parameters: 
#    individual_set_id = COAD
#    mutation_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.maf
#    coverage_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.coverage.mat
#    patient_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/COAD/1910000/0.MutSigPreprocess.Finished/COAD.patients.txt
#    category_file = file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/ProcessCoverageForMutSig/COAD/1910172/0.ProcessCoverageForMutSig.Finished/COAD.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/COAD/1910000/0.MutSigPreprocess.Finished/COAD.mutation_preprocessing_report.txt
#    jobcount = 200
