Example usage for java.lang Package.Args Package.Args

Introduction

In this page you can find the example usage for java.lang Package.Args Package.Args.

Prototype

Package.Args

Source Link

Usage

From source file:uk.ac.tgac.citadel.CitadelPipeline.java

public void init() throws IOException {

    // Configure pipeline
    this.clearProcessList();

    Args args = this.getArgs();

    // Clear pipeline
    this.clearProcessList();

    // Stage 1: Alignment
    File decompressDir = new File(this.args.getOutputDir(), "1-decompress");
    Decompress.Args decompressArgs = new Decompress.Args();
    decompressArgs.setOutputDir(decompressDir);
    decompressArgs.setJobPrefix(args.getJobPrefix() + "-decompress");
    decompressArgs.setRunParallel(args.isRunParallel());
    decompressArgs.setPaired(args.isPaired());
    decompressArgs.setRecursive(args.isRecursive());

    if (this.args.stages.contains(CitadelStage.DECOMPRESS)) {
        this.addProcess(new Decompress(this.conanExecutorService, decompressArgs));
    }//from w w w .j  a v  a2  s  .co  m

    // Stage 2: Jellyswarm
    File jellyswarmDir = new File(this.args.getOutputDir(), "2-jellyswarm");
    Jellyswarm.Args jellyswarmArgs = new Jellyswarm.Args();
    jellyswarmArgs.setOutputDir(jellyswarmDir);
    jellyswarmArgs.setJobPrefix(args.getJobPrefix() + "-jellyswarm");
    jellyswarmArgs.setThreads(args.getThreadsPerProcess());
    jellyswarmArgs.setRunParallel(args.isRunParallel());
    jellyswarmArgs.setInputDir(decompressDir);
    jellyswarmArgs.setLowerCount(2);
    jellyswarmArgs.setHashSize(400000000L);
    jellyswarmArgs.setPaired(args.isPaired());

    if (this.args.stages.contains(CitadelStage.JELLYSWARM)) {
        this.addProcess(new Jellyswarm(this.conanExecutorService, jellyswarmArgs));
    }

    // Stage 3: RAMPART (works out which samples to analyse by itself)
    File rampartDir = new File(this.args.getOutputDir(), "3-rampart");
    Rampart.Args rampartArgs = new Rampart.Args();
    rampartArgs.setOutputDir(rampartDir);
    rampartArgs.setJobPrefix(args.getJobPrefix() + "-rampart");
    rampartArgs.setOrganism(args.getOrganism());

    if (this.args.stages.contains(CitadelStage.RAMPART)) {
        this.addProcess(new Rampart(this.conanExecutorService, rampartArgs));
    }

    // Stage 4: Run transdecoder on cufflinks and pasa output

    File assembleDir = new File(this.args.getOutputDir(), "4-assemble");
    Assemble.Args assembleArgs = new Assemble.Args();
    assembleArgs.setOutputDir(assembleDir);
    assembleArgs.setJobPrefix(args.getJobPrefix() + "-assemble");
    assembleArgs.setRunParallel(args.isRunParallel());

    if (this.args.stages.contains(CitadelStage.ASSEMBLE)) {
        this.addProcess(new Assemble(this.conanExecutorService, assembleArgs));
    }

    // Stage 5: Annotate assemblies
    File annotateDir = new File(this.args.getOutputDir(), "5-annotate");
    Annotate.Args annotateArgs = new Annotate.Args();
    annotateArgs.setOutputDir(annotateDir);
    annotateArgs.setJobPrefix(args.getJobPrefix() + "-annotate");
    annotateArgs.setRunParallel(args.isRunParallel());

    if (this.args.stages.contains(CitadelStage.ANNOTATE)) {
        this.addProcess(new Annotate(this.conanExecutorService, annotateArgs));
    }

    // Stage 5: Annotate assemblies
    File packageDir = new File(this.args.getOutputDir(), "6-package");
    Package.Args packageArgs = new Package.Args();
    packageArgs.setOutputDir(packageDir);
    packageArgs.setJobPrefix(args.getJobPrefix() + "-package");
    packageArgs.setRunParallel(args.isRunParallel());

    if (this.args.stages.contains(CitadelStage.PACKAGE)) {
        this.addProcess(new Package(this.conanExecutorService, packageArgs));
    }

    // Check all processes in the pipeline are operational, modify execution context to execute unscheduled locally
    ExecutionContext localContext = new DefaultExecutionContext(new Local(), null,
            this.conanExecutorService.getExecutionContext().getExternalProcessConfiguration());

    if (!this.isOperational(localContext)) {
        throw new IOException(
                "The pipeline contains one or more processes that are not currently operational.  "
                        + "Please fix before restarting pipeline.");
    }
}

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