72 lines
3.5 KiB
Scala
72 lines
3.5 KiB
Scala
/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.queue.engine
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import java.io.File
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import org.broadinstitute.sting.queue.QSettings
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import org.broadinstitute.sting.commandline.{ArgumentCollection, Argument}
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import org.broadinstitute.sting.queue.util.SystemUtils
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/**
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* Command line options for a QGraph.
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*/
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class QGraphSettings {
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@Argument(fullName="run_scripts", shortName="run", doc="Run QScripts. Without this flag set only performs a dry run.", required=false)
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var run = false
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@Argument(fullName="job_runner", shortName="jobRunner", doc="Use the specified job runner to dispatch command line jobs", required=false)
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var jobRunner: String = _
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@Argument(fullName="bsub", shortName="bsub", doc="Equivalent to -jobRunner Lsf706", required=false)
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var bsub = false
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@Argument(fullName="status",shortName="status",doc="Get status of jobs for the qscript",required=false)
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var getStatus = false
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@Argument(fullName="retry_failed", shortName="retry", doc="Retry the specified number of times after a command fails. Defaults to no retries.", required=false)
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var retries = 0
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@Argument(fullName="start_from_scratch", shortName="startFromScratch", doc="Runs all command line functions even if the outputs were previously output successfully.", required=false)
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var startFromScratch = false
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@Argument(fullName="keep_intermediate_outputs", shortName="keepIntermediates", doc="After a successful run keep the outputs of any Function marked as intermediate.", required=false)
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var keepIntermediates = false
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@Argument(fullName="status_email_to", shortName="statusTo", doc="Email address to send emails to upon completion or on error.", required=false)
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var statusEmailTo: List[String] = Nil
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@Argument(fullName="status_email_from", shortName="statusFrom", doc="Email address to send emails from upon completion or on error.", required=false)
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var statusEmailFrom: String = System.getProperty("user.name") + "@" + SystemUtils.mailName
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@Argument(fullName="dot_graph", shortName="dot", doc="Outputs the queue graph to a .dot file. See: http://en.wikipedia.org/wiki/DOT_language", required=false)
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var dotFile: File = _
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@Argument(fullName="expanded_dot_graph", shortName="expandedDot", doc="Outputs the queue graph of scatter gather to a .dot file. Otherwise overwrites the dot_graph", required=false)
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var expandedDotFile: File = _
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@ArgumentCollection
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val qSettings = new QSettings
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}
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