24 lines
1.0 KiB
Python
24 lines
1.0 KiB
Python
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import os
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import JobDispatcher
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PRINT_ONLY = True
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QUEUES = ["gsa","short","long"]
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LIMITS = dict([["gsa",50],["short",20],["long",50]])
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ACTION = "space"
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TIME_DIFF = "0:1:0" # 1 hour
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RESULTS_DIR = "/humgen/gsa-hpprojects/dev/kiran/wholeExomeGeneCoverage/scratch/"
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GATK_JAR = "/humgen/gsa-scr1/chartl/sting/dist/GenomeAnalysisTK.jar"
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MEMORY = "2g"
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WALKER = "CoverageStatistics"
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REFERENCE = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
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BAM_FILES = RESULTS_DIR+"bam_files_use.list"
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INTERVAL_LIST = "/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_exome_agilent_designed_120.targets.interval_list"
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MAX_BASES_PER_JOB = 100000
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ARGUMENTS = "-mmq 20 -mbq 10 -omitBaseOutput -dels -l INFO"
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dispatcher = JobDispatcher.GATKDispatcher(GATK_JAR,MEMORY,WALKER,ARGUMENTS,RESULTS_DIR,REFERENCE,
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BAM_FILES,INTERVAL_LIST,QUEUES,LIMITS,PRINT_ONLY,ACTION,TIME_DIFF)
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dispatcher.setProject("GSA_WholeExome_CoverageByExon")
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dispatcher.dispatchByInterval(MAX_BASES_PER_JOB)
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