# Created: Thu Mar 29 07:06:26 EDT 2012 by cgaadm_deadline
# Job: 68685    server:  http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/
# Module: MutSigRun urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:120
# Parameters: 
#    individual_set_id = STAD
#    mutation_file = STAD.maf   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/68683/STAD.maf
#    coverage_file = STAD.coverage.mat   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/68684/STAD.coverage.mat
#    patient_file = STAD.patients.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/68683/STAD.patients.txt
#    category_file = STAD.mutcategs.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/68684/STAD.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 = STAD.mutation_preprocessing_report.txt   http://tcga-gdac-genepattern.broadinstitute.org:8090/gp/jobResults/68683/STAD.mutation_preprocessing_report.txt
#    jobcount = 200
