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Fix merge conflicts
2 parents 4f79845 + 4611fc8 commit 23a04a1

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‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractCommandWrapper.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -289,7 +289,7 @@ protected boolean isThrowNonZeroExits()
289289
return _throwNonZeroExits;
290290
}
291291

292-
protected static File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
292+
public static File resolveFileInPath(String exe, @Nullable String packageName, boolean throwIfNotFound)
293293
{
294294
File fn;
295295
String path;

‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -90,6 +90,7 @@ public List<String> getBaseArgs(@Nullable String toolName)
9090
List<String> args = new ArrayList<>();
9191
args.add(SequencePipelineService.get().getJavaFilepath());
9292
args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
93+
args.add("-DGATK_STACKTRACE_ON_USER_EXCEPTION=true");
9394
args.add("-jar");
9495
args.add(getJAR().getPath());
9596

@@ -98,6 +99,8 @@ public List<String> getBaseArgs(@Nullable String toolName)
9899
args.add(toolName);
99100
}
100101

102+
103+
101104
return args;
102105
}
103106

‎SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java‎

Lines changed: 110 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,110 @@
1+
package org.labkey.api.sequenceanalysis.run;
2+
3+
import org.apache.commons.io.FileUtils;
4+
import org.apache.commons.lang3.StringUtils;
5+
import org.apache.logging.log4j.Logger;
6+
import org.labkey.api.pipeline.PipelineJobException;
7+
import org.labkey.api.sequenceanalysis.pipeline.PipelineOutputTracker;
8+
import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
9+
import org.labkey.api.writer.PrintWriters;
10+
11+
import java.io.File;
12+
import java.io.IOException;
13+
import java.io.PrintWriter;
14+
import java.util.Arrays;
15+
import java.util.List;
16+
17+
public class DockerWrapper extends AbstractCommandWrapper
18+
{
19+
private final String _containerName;
20+
private File _tmpDir = null;
21+
22+
public DockerWrapper(String containerName, Logger log)
23+
{
24+
super(log);
25+
_containerName = containerName;
26+
}
27+
28+
public void setTmpDir(File tmpDir)
29+
{
30+
_tmpDir = tmpDir;
31+
}
32+
33+
public void executeWithDocker(List<String> containerArgs, File workDir, PipelineOutputTracker tracker) throws PipelineJobException
34+
{
35+
File localBashScript = new File(workDir, "docker.sh");
36+
File dockerBashScript = new File(workDir, "dockerRun.sh");
37+
tracker.addIntermediateFile(localBashScript);
38+
tracker.addIntermediateFile(dockerBashScript);
39+
40+
setWorkingDir(workDir);
41+
try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript); PrintWriter dockerWriter = PrintWriters.getPrintWriter(dockerBashScript))
42+
{
43+
writer.println("#!/bin/bash");
44+
writer.println("set -x");
45+
writer.println("WD=`pwd`");
46+
writer.println("HOME=`echo ~/`");
47+
writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'");
48+
writer.println("sudo $DOCKER pull " + _containerName);
49+
writer.println("sudo $DOCKER run --rm=true \\");
50+
writer.println("\t-v \"${WD}:/work\" \\");
51+
writer.println("\t-v \"${HOME}:/homeDir\" \\");
52+
if (_tmpDir != null)
53+
{
54+
writer.println("\t-v \"" + _tmpDir.getPath() + ":/tmp\" \\");
55+
}
56+
writer.println("\t--entrypoint /bin/bash \\");
57+
writer.println("\t-w /work \\");
58+
Integer maxRam = SequencePipelineService.get().getMaxRam();
59+
if (maxRam != null)
60+
{
61+
writer.println("\t-e SEQUENCEANALYSIS_MAX_RAM=" + maxRam + " \\");
62+
writer.println("\t--memory='" + maxRam + "g' \\");
63+
}
64+
writer.println("\t" + _containerName + " \\");
65+
writer.println("\t/work/" + dockerBashScript.getName());
66+
writer.println("EXIT_CODE=$?");
67+
writer.println("echo 'Docker run exit code: '$EXIT_CODE");
68+
writer.println("exit $EXIT_CODE");
69+
70+
dockerWriter.println("#!/bin/bash");
71+
dockerWriter.println("set -x");
72+
dockerWriter.println(StringUtils.join(containerArgs, " "));
73+
dockerWriter.println("EXIT_CODE=$?");
74+
dockerWriter.println("echo 'Exit code: '$?");
75+
dockerWriter.println("exit $EXIT_CODE");
76+
}
77+
catch (IOException e)
78+
{
79+
throw new PipelineJobException(e);
80+
}
81+
82+
execute(Arrays.asList("/bin/bash", localBashScript.getPath()));
83+
}
84+
85+
public File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTracker output) throws PipelineJobException
86+
{
87+
try
88+
{
89+
if (workingDirectory.equals(input.getParentFile()))
90+
{
91+
return input;
92+
}
93+
94+
File local = new File(workingDirectory, input.getName());
95+
if (!local.exists())
96+
{
97+
getLogger().debug("Copying file locally: " + input.getPath());
98+
FileUtils.copyFile(input, local);
99+
}
100+
101+
output.addIntermediateFile(local);
102+
103+
return local;
104+
}
105+
catch (IOException e)
106+
{
107+
throw new PipelineJobException(e);
108+
}
109+
}
110+
}

‎SequenceAnalysis/pipeline_code/sequence_tools_install.sh‎

Lines changed: 4 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -335,30 +335,6 @@ else
335335
fi
336336

337337

338-
#
339-
# BisSNP
340-
#
341-
echo ""
342-
echo ""
343-
echo "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%"
344-
echo "Install BisSNP"
345-
echo ""
346-
cd $LKSRC_DIR
347-
348-
if [[ ! -e ${LKTOOLS_DIR}/BisSNP.jar || ! -z $FORCE_REINSTALL ]];
349-
then
350-
echo "Cleaning up previous installs"
351-
rm -Rf BisSNP*
352-
rm -Rf $LKTOOLS_DIR/BisSNP.jar
353-
354-
wget $WGET_OPTS https://downloads.sourceforge.net/project/bissnp/BisSNP-0.82.2/BisSNP-0.82.2.jar
355-
356-
install ./BisSNP-0.82.2.jar $LKTOOLS_DIR/BisSNP.jar
357-
else
358-
echo "Already installed"
359-
fi
360-
361-
362338
#
363339
#mosaik
364340
#
@@ -510,10 +486,10 @@ then
510486
rm -Rf bcftools*
511487
rm -Rf $LKTOOLS_DIR/bcftools
512488

513-
wget $WGET_OPTS https://github.com/samtools/bcftools/releases/download/1.18/bcftools-1.18.tar.bz2
514-
tar xjvf bcftools-1.18.tar.bz2
515-
chmod 755 bcftools-1.18
516-
cd bcftools-1.18
489+
wget $WGET_OPTS https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
490+
tar xjvf bcftools-1.20.tar.bz2
491+
chmod 755 bcftools-1.20
492+
cd bcftools-1.20
517493
rm -f plugins/liftover.c
518494
wget $WGET_OPTS -P plugins https://raw.githubusercontent.com/freeseek/score/master/liftover.c
519495

‎SequenceAnalysis/resources/queries/sequenceanalysis/chain_files/.qview.xml‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
2+
<columns>
3+
<!--<column name="rowid" />-->
4+
<column name="genomeId1" />
5+
<column name="genomeId2" />
6+
<column name="source" />
7+
<column name="version" />
8+
<column name="datedisabled" />
9+
<column name="chainFile" />
10+
</columns>
11+
<sorts>
12+
<sort column="genomeId1/name"/>
13+
<sort column="genomeId2/name"/>
14+
<sort column="version"/>
15+
</sorts>
16+
</customView>

‎SequenceAnalysis/resources/queries/sequenceanalysis/chain_files/With Filepath.qview.xml‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
<customView xmlns="http://labkey.org/data/xml/queryCustomView">
2+
<columns>
3+
<!--<column name="rowid" />-->
4+
<column name="genomeId1" />
5+
<column name="genomeId2" />
6+
<column name="source" />
7+
<column name="version" />
8+
<column name="dateDisabled" />
9+
<column name="chainFile" />
10+
<column name="chainFile/DataFileUrl" />
11+
</columns>
12+
<sorts>
13+
<sort column="genomeId1/name"/>
14+
<sort column="genomeId2/name"/>
15+
<sort column="version"/>
16+
</sorts>
17+
</customView>

‎SequenceAnalysis/resources/web/SequenceAnalysis/panel/BaseSequencePanel.js‎

Lines changed: 1 addition & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -269,9 +269,6 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
269269
return;
270270
}
271271

272-
// If auto-loading, assume we want to read the URL
273-
thePanel.down('#readUrlParams').setValue(true);
274-
275272
var recIdx = store.find('name', LABKEY.ActionURL.getParameter('template'));
276273
if (recIdx > -1) {
277274
thePanel.down('labkey-combo').setValue(store.getAt(recIdx));
@@ -300,12 +297,6 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
300297
helpPopup: 'By default, the pipelines jobs and their outputs will be created in the workbook you selected. However, in certain cases, such as bulk submission of many jobs, it might be preferable to submit each job to the source folder/workbook for each input. Checking this box will enable this.',
301298
fieldLabel: 'Submit Jobs to Same Folder/Workbook as Readset',
302299
labelWidth: 200
303-
},{
304-
xtype: 'checkbox',
305-
itemId: 'readUrlParams',
306-
helpPopup: 'If true, any parameters provided on the URL with the same name as a parameter in the JSON will be read and override the template.',
307-
fieldLabel: 'Read Parameters From URL',
308-
labelWidth: 200
309300
}]
310301
}],
311302
buttons: [{
@@ -362,8 +353,7 @@ Ext4.define('SequenceAnalysis.panel.BaseSequencePanel', {
362353
delete json.submitJobToReadsetContainer;
363354
}
364355

365-
var readUrlParams = win.down('#readUrlParams').getValue();
366-
win.sequencePanel.applySavedValues(json, readUrlParams);
356+
win.sequencePanel.applySavedValues(json, true);
367357

368358
var submitJobToReadsetContainer = win.sequencePanel.down('[name="submitJobToReadsetContainer"]');
369359
if (submitJobToReadsetContainer) {

‎SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js‎

Lines changed: 19 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -104,14 +104,24 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
104104
maxValue: 1.0,
105105
value: 0.95,
106106
fieldLabel: 'Min Percent Match',
107-
helpPopup: 'In order to lift to the target genome, the feature must have at least this percent match. Lower this value to be more permissive; however, this risks incorrect liftovers',
107+
helpPopup: 'In order to lift to the target genome, the feature must have at least this percent match. Lower this value to be more permissive; however, this risks incorrect liftovers. This is ignored if using bcftools.',
108108
itemId: 'pctField'
109109
},{
110110
xtype: 'checkbox',
111111
itemId: 'dropGenotypes',
112112
checked: false,
113113
helpPopup: 'If checked, no genotypes will be written to the output file (applies to VCFs only). This can be useful (and necessary) when lifting VCFs with extremely high sample number.',
114114
fieldLabel: 'Drop Genotypes'
115+
},{
116+
xtype: 'checkbox',
117+
itemId: 'useBcfTools',
118+
checked: false,
119+
fieldLabel: 'Use bcftools'
120+
},{
121+
xtype: 'checkbox',
122+
itemId: 'doNotRetainUnmapped',
123+
checked: false,
124+
fieldLabel: 'Do Not Retain Unmapped'
115125
}].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)),
116126
buttons: [{
117127
text: 'Submit',
@@ -152,6 +162,14 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
152162
params.dropGenotypes = this.down('#dropGenotypes').getValue();
153163
}
154164

165+
if (this.down('#useBcfTools').getValue()){
166+
params.useBcfTools = this.down('#useBcfTools').getValue();
167+
}
168+
169+
if (this.down('#doNotRetainUnmapped').getValue()){
170+
params.doNotRetainUnmapped = this.down('#doNotRetainUnmapped').getValue();
171+
}
172+
155173
Ext4.Msg.wait('Saving...');
156174
LABKEY.Ajax.request({
157175
url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler', this.containerPath),

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -59,6 +59,7 @@
5959
import org.labkey.sequenceanalysis.analysis.RnaSeqcHandler;
6060
import org.labkey.sequenceanalysis.analysis.SbtGeneCountHandler;
6161
import org.labkey.sequenceanalysis.analysis.UnmappedSequenceBasedGenotypeHandler;
62+
import org.labkey.sequenceanalysis.analysis.UpdateReadsetFilesHandler;
6263
import org.labkey.sequenceanalysis.button.AddSraRunButton;
6364
import org.labkey.sequenceanalysis.button.ArchiveReadsetsButton;
6465
import org.labkey.sequenceanalysis.button.ChangeReadsetStatusButton;
@@ -77,6 +78,7 @@
7778
import org.labkey.sequenceanalysis.run.alignment.BowtieWrapper;
7879
import org.labkey.sequenceanalysis.run.alignment.GSnapWrapper;
7980
import org.labkey.sequenceanalysis.run.alignment.MosaikWrapper;
81+
import org.labkey.sequenceanalysis.run.alignment.ParagraphStep;
8082
import org.labkey.sequenceanalysis.run.alignment.Pbmm2Wrapper;
8183
import org.labkey.sequenceanalysis.run.alignment.StarWrapper;
8284
import org.labkey.sequenceanalysis.run.alignment.VulcanWrapper;
@@ -113,6 +115,7 @@
113115
import org.labkey.sequenceanalysis.run.util.FastqcRunner;
114116
import org.labkey.sequenceanalysis.run.util.GenomicsDBAppendHandler;
115117
import org.labkey.sequenceanalysis.run.util.GenomicsDBImportHandler;
118+
import org.labkey.sequenceanalysis.run.util.SVAnnotateStep;
116119
import org.labkey.sequenceanalysis.run.variant.*;
117120
import org.labkey.sequenceanalysis.util.Barcoder;
118121
import org.labkey.sequenceanalysis.util.ChainFileValidator;
@@ -299,6 +302,7 @@ public static void registerPipelineSteps()
299302
SequencePipelineService.get().registerPipelineStep(new MendelianViolationReportStep.Provider());
300303
SequencePipelineService.get().registerPipelineStep(new SummarizeGenotypeQualityStep.Provider());
301304
SequencePipelineService.get().registerPipelineStep(new BcftoolsFillTagsStep.Provider());
305+
SequencePipelineService.get().registerPipelineStep(new SVAnnotateStep.Provider());
302306

303307
//handlers
304308
SequenceAnalysisService.get().registerFileHandler(new LiftoverHandler());
@@ -333,6 +337,8 @@ public static void registerPipelineSteps()
333337
SequenceAnalysisService.get().registerFileHandler(new PbsvJointCallingHandler());
334338
SequenceAnalysisService.get().registerFileHandler(new DeepVariantHandler());
335339
SequenceAnalysisService.get().registerFileHandler(new GLNexusHandler());
340+
SequenceAnalysisService.get().registerFileHandler(new ParagraphStep());
341+
SequenceAnalysisService.get().registerFileHandler(new UpdateReadsetFilesHandler());
336342

337343
SequenceAnalysisService.get().registerReadsetHandler(new MultiQCHandler());
338344
SequenceAnalysisService.get().registerReadsetHandler(new RestoreSraDataHandler());

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