When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.
Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory. Updated various tests for above items and other small fixes.
This commit is contained in:
Khalid Shakir
parent
e5df9e0684
commit
7486696c07
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@ -109,7 +109,7 @@ public class RScriptExecutor {
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List<File> tempFiles = new ArrayList<File>();
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try {
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File tempLibDir = IOUtils.tempDir("R.", ".lib");
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File tempLibDir = IOUtils.tempDir("Rlib.", "");
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tempFiles.add(tempLibDir);
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StringBuilder expression = new StringBuilder("tempLibDir = '").append(tempLibDir).append("';");
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@ -79,7 +79,7 @@ public class IOUtils {
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tempDirParent = FileUtils.getTempDirectory();
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if (!tempDirParent.exists() && !tempDirParent.mkdirs())
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throw new UserException.BadTmpDir("Could not create temp directory: " + tempDirParent);
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File temp = File.createTempFile(prefix + "-", suffix, tempDirParent);
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File temp = File.createTempFile(prefix, suffix, tempDirParent);
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if (!temp.delete())
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throw new UserException.BadTmpDir("Could not delete sub file: " + temp.getAbsolutePath());
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if (!temp.mkdir())
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@ -3,9 +3,11 @@ package org.broadinstitute.sting;
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import org.apache.commons.io.FileUtils;
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import org.apache.log4j.*;
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import org.apache.log4j.spi.LoggingEvent;
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import org.apache.xmlbeans.impl.common.IOUtil;
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import org.broadinstitute.sting.commandline.CommandLineUtils;
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import org.broadinstitute.sting.gatk.walkers.diffengine.DiffEngine;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.io.IOUtils;
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import org.testng.Assert;
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import javax.swing.*;
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@ -78,8 +80,8 @@ public abstract class BaseTest {
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public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
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public static final String hg19Chr20Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
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public static final String networkTempDir = "/broad/shptmp/" + System.getProperty("user.name") + "/";
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public static final File networkTempDirFile = new File(networkTempDir);
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public static final String networkTempDir;
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public static final File networkTempDirFile;
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public static final File testDirFile = new File("public/testdata/");
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public static final String testDir = testDirFile.getAbsolutePath() + "/";
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@ -99,6 +101,10 @@ public abstract class BaseTest {
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// Set the Root logger to only output warnings.
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logger.setLevel(Level.WARN);
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networkTempDirFile = IOUtils.tempDir("temp.", ".dir", new File("/broad/shptmp/" + System.getProperty("user.name")));
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networkTempDirFile.deleteOnExit();
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networkTempDir = networkTempDirFile.getAbsolutePath() + "/";
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// find our file sources
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// if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
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// logger.fatal("We can't locate the reference directories. Aborting!");
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@ -233,18 +239,12 @@ public abstract class BaseTest {
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/**
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* Creates a temp file that will be deleted on exit after tests are complete.
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* @param name Prefix of the file.
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* @param extension Extension to concat to the end of the file.
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* @return A file in the network temporary directory starting with name, ending with extension, which will be deleted after the program exits.
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* @param name Name of the file.
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* @return A file in the network temporary directory with name, which will be deleted after the program exits.
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*/
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public static File createNetworkTempFile(String name, String extension) {
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try {
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FileUtils.forceMkdir(networkTempDirFile);
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File file = File.createTempFile(name, extension, networkTempDirFile);
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file.deleteOnExit();
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return file;
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} catch (IOException ex) {
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throw new ReviewedStingException("Cannot create temp file: " + ex.getMessage(), ex);
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}
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public static File createNetworkTempFile(String name) {
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File file = new File(networkTempDirFile, name);
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file.deleteOnExit();
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return file;
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}
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}
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@ -62,7 +62,7 @@ public class JnaSessionIntegrationTest extends BaseTest {
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return;
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}
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File outFile = createNetworkTempFile("JnaSessionIntegrationTest-", ".out");
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File outFile = createNetworkTempFile("JnaSessionIntegrationTest.out");
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Session session = factory.getSession();
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session.init(null);
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try {
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@ -86,7 +86,7 @@ public class LibDrmaaIntegrationTest extends BaseTest {
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@Test(dependsOnMethods = { "testDrmaa" })
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public void testSubmitEcho() throws Exception {
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if (implementation.indexOf("LSF") >= 0) {
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if (implementation.contains("LSF")) {
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System.err.println(" *********************************************************");
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System.err.println(" ***********************************************************");
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System.err.println(" **** ****");
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@ -101,7 +101,7 @@ public class LibDrmaaIntegrationTest extends BaseTest {
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Memory error = new Memory(LibDrmaa.DRMAA_ERROR_STRING_BUFFER);
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int errnum;
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File outFile = createNetworkTempFile("LibDrmaaIntegrationTest-", ".out");
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File outFile = createNetworkTempFile("LibDrmaaIntegrationTest.out");
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errnum = LibDrmaa.drmaa_init(null, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN);
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@ -93,7 +93,7 @@ public class LibBatIntegrationTest extends BaseTest {
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@Test
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public void testSubmitEcho() throws Exception {
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String queue = "hour";
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File outFile = createNetworkTempFile("LibBatIntegrationTest-", ".out");
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File outFile = createNetworkTempFile("LibBatIntegrationTest.out");
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submit req = new submit();
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@ -19,7 +19,7 @@ class ExampleCountLoci extends QScript {
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@Output
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var out: File = _
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def script = {
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def script() {
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val countLoci = new CountLoci
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countLoci.reference_sequence = referenceFile
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countLoci.input_file = bamFiles
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@ -24,7 +24,7 @@ class ExampleCountReads extends QScript {
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/**
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* In script, you create and then add() functions to the pipeline.
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*/
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def script = {
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def script() {
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// Run CountReads for all bams jointly.
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@ -41,6 +41,9 @@ class ExampleCountReads extends QScript {
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// matches the full form of the argument, but will actually be a scala List[]
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jointCountReads.input_file = bamFiles
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// Set the memory limit. Also acts as a memory request on LSF and GridEngine.
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jointCountReads.memoryLimit = 1
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// Add the newly created function to the pipeline.
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add(jointCountReads)
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@ -51,6 +54,7 @@ class ExampleCountReads extends QScript {
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singleCountReads.reference_sequence = referenceFile
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// ':+' is the scala List append operator
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singleCountReads.input_file :+= bamFile
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singleCountReads.memoryLimit = 1
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add(singleCountReads)
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}
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}
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@ -24,7 +24,7 @@ class ExampleCustomWalker extends QScript {
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/**
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* In script, you create and then add() functions to the pipeline.
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*/
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def script = {
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def script() {
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val customWalker = new CommandLineGATK {
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// Set the name of your walker, for example this will be passed as -T MyCustomWalker
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this.analysis_type = "MyCustomWalker"
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@ -33,7 +33,6 @@ class ExampleUnifiedGenotyper extends QScript {
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@Argument(doc="An optional list of filter expressions.", shortName="filterExpression", required=false)
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var filterExpressions: List[String] = Nil
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// This trait allows us set the variables below in one place,
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// and then reuse this trait on each CommandLineGATK function below.
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trait UnifiedGenotyperArguments extends CommandLineGATK {
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@ -89,7 +89,7 @@ class QCommandLine extends CommandLineProgram with Logging {
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private var shuttingDown = false
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private lazy val pluginManager = {
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qScriptClasses = IOUtils.tempDir("Q-Classes", "", settings.qSettings.tempDirectory)
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qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
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qScriptManager.loadScripts(scripts, qScriptClasses)
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new PluginManager[QScript](classOf[QScript], List(qScriptClasses.toURI.toURL))
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}
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@ -30,7 +30,7 @@ import org.broadinstitute.sting.BaseTest
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class ExampleCountLociPipelineTest {
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@Test
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def testCountLoci {
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def testCountLoci() {
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val testOut = "count.out"
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val spec = new PipelineTestSpec
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spec.name = "countloci"
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@ -0,0 +1,66 @@
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/*
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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.pipeline.examples
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/*
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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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import org.testng.annotations.Test
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import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
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import org.broadinstitute.sting.BaseTest
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class ExampleCountReadsPipelineTest {
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@Test
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def testCountReads() {
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val spec = new PipelineTestSpec
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spec.name = "countreads"
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spec.args = Array(
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" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala",
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" -R " + BaseTest.testDir + "exampleFASTA.fasta",
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" -I " + BaseTest.testDir + "exampleBAM.bam").mkString
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PipelineTest.executeTest(spec)
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}
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}
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@ -0,0 +1,92 @@
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/*
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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.pipeline.examples
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/*
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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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/*
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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,
|
||||
* 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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import org.testng.annotations.Test
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import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
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import org.broadinstitute.sting.BaseTest
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class ExampleUnifiedGenotyperPipelineTest {
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@Test
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def testUnifiedGenotyper() {
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val spec = new PipelineTestSpec
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spec.name = "unifiedgenotyper"
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spec.args = Array(
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" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
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" -R " + BaseTest.testDir + "exampleFASTA.fasta",
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" -I " + BaseTest.testDir + "exampleBAM.bam",
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" -filter QD",
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" -filterExpression 'QD < 2.0'").mkString
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PipelineTest.executeTest(spec)
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}
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}
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Reference in New Issue