# Created: Fri May 04 20:43:50 EDT 2012 by cgaadm
# Job: 84402    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:120
# Parameters: 
#    individual_set_id = BLCA
#    mutation_file = BLCA.maf   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/84400/BLCA.maf
#    coverage_file = BLCA.coverage.mat   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/84401/BLCA.coverage.mat
#    patient_file = BLCA.patients.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/84400/BLCA.patients.txt
#    category_file = BLCA.mutcategs.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/84401/BLCA.mutcategs.txt
#    gene_list = /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt
#    build = hg18
#    geneset_file = /xchip/tcga/gbm/analysis/lawrence/db/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
#    genome_dir = /xchip/cga1/annotation/db/ucsc/hg18
#    param_file = /xchip/cga1/reference/mutsig_params/MutSig1.5.params.txt
#    mutation_preprocessing_report_file = BLCA.mutation_preprocessing_report.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/84400/BLCA.mutation_preprocessing_report.txt
#    jobcount = 200
