Compiling GATK External Example

arcolomboarcolombo LAMember
edited January 2017 in Ask the GATK team

Hi so i'm using UBUNTU 14.04 with mvn 3.3.9 and i've cloned the GATK-protected from github. From the previous forum posts I'm not using the command `git reset --hard 3.1' and am using the raw gatk clone.
I keep failing on the external example error when compiling gatk-protected clone.

c/external-example/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] GATK Root ......................................... SUCCESS [0.738s]
[INFO] GATK Aggregator ................................... SUCCESS [0.564s]
[INFO] GATK GSALib ....................................... SUCCESS [0.523s]
[INFO] GATK Utils ........................................ SUCCESS [4.657s]
[INFO] GATK Engine ....................................... SUCCESS [2.112s]
[INFO] GATK Tools Public ................................. SUCCESS [5.022s]
[INFO] External Example .................................. FAILURE [0.354s]
[INFO] GATK Aggregator Public ............................ SKIPPED
[INFO] GATK Tools Protected .............................. SKIPPED
[INFO] GATK Package Distribution ......................... SKIPPED
[INFO] GATK Aggregator Protected ......................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 14.252s
[INFO] Finished at: Tue Jan 03 11:40:29 PST 2017
[INFO] Final Memory: 41M/323M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile) on project external-example: Compilation failure: Compilation failure:
[ERROR] /home/arcolombo/Documents/gatk-protected/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java:[39,48] error: generics are not supported in -source 1.3
[ERROR]
[ERROR] (use -source 5 or higher to enable generics)
[ERROR] /home/arcolombo/Documents/gatk-protected/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java:[40,5] error: annotations are not supported in -source 1.3
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn -rf :external-example

If I try to untar the intelliJ example I get errors

arcolombo@arcolombo-ThinkPad-T450s:~/Documents/gatk-protected$ sudo tar xvfj intellij_example.tar.bz2
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/.name
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/ant.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/codeStyleSettings.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/compiler.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/copyright/
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/dictionaries/
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/encodings.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/highlighting.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/inspectionProfiles/
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.creationtime'
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/libraries/
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/misc.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/modules.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/scopes/
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/uiDesigner.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/vcs.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/workspace.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/scopes/scope_settings.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/libraries/GATK_libraries.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/inspectionProfiles/profiles_settings.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/inspectionProfiles/Project_Default.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
.idea/copyright/profiles_settings.xml
tar: Ignoring unknown extended header keyword 'SCHILY.dev'
tar: Ignoring unknown extended header keyword 'SCHILY.ino'
tar: Ignoring unknown extended header keyword 'SCHILY.nlink'
cmi-gatk.iml
arcolombo@arcolombo-ThinkPad-T450s:~/Documents/gatk-protected$

I have intelliJ installed

idea.sh
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=350m; support was removed in 8.0

java -version
java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

mvn -version
Apache Maven 3.3.9 (bb52d8502b132ec0a5a3f4c09453c07478323dc5; 2015-11-10T08:41:47-08:00)
Maven home: /usr/local/apache-maven-3.3.9
Java version: 1.8.0_111, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-8-oracle/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "4.4.0-57-generic", arch: "amd64", family: "unix"

I am not sure how to compile GATK from scratch. trying to set up the mutect install.

when I attempt to import GATK-protected git clone directory to INTELLIJ I receive the following error
64-Bit Server VM (build 25.111-b14, mixed mode)
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=350m; support was removed in 8.0
Failed to clear URL cache
Failed to clear URL cache
[ 46765] ERROR - com.intellij.ide.IdeEventQueue - Error during dispatching of java.awt.event.MouseEvent[MOUSE_RELEASED,(249,257),absolute(895,465),button=1,modifiers=Button1,clickCount=1] on frame0
java.lang.ClassCastException: sun.font.CompositeFont cannot be cast to sun.font.PhysicalFont
at sun.font.CompositeFont.doDeferredInitialisation(CompositeFont.java:274)
at sun.font.CompositeFont.getSlotFont(CompositeFont.java:341)
at sun.font.CompositeGlyphMapper.getSlotMapper(CompositeGlyphMapper.java:114)
at sun.font.CompositeGlyphMapper.convertToGlyph(CompositeGlyphMapper.java:124)
at sun.font.CompositeGlyphMapper.charToGlyph(CompositeGlyphMapper.java:162)
at sun.font.CompositeStrike.getCodePointAdvance(CompositeStrike.java:158)
at sun.font.FontDesignMetrics.handleCharWidth(FontDesignMetrics.java:416)
at sun.font.FontDesignMetrics.getLatinCharWidth(FontDesignMetrics.java:425)
at sun.font.FontDesignMetrics.stringWidth(FontDesignMetrics.java:476)
at sun.swing.SwingUtilities2.stringWidth(SwingUtilities2.java:403)
at javax.swing.SwingUtilities.layoutCompoundLabelImpl(SwingUtilities.java:1005)
at javax.swing.SwingUtilities.layoutCompoundLabel(SwingUtilities.java:890)
at javax.swing.plaf.basic.BasicGraphicsUtils.getPreferredButtonSize(BasicGraphicsUtils.java:282)
at javax.swing.plaf.basic.BasicButtonUI.getPreferredSize(BasicButtonUI.java:376)
at javax.swing.JComponent.getPreferredSize(JComponent.java:1662)
at org.jetbrains.idea.maven.wizards.MavenProjectImportStep.(MavenProjectImportStep.java:84)
at org.jetbrains.idea.maven.wizards.MavenProjectImportProvider.createSteps(MavenProjectImportProvider.java:45)
at com.intellij.projectImport.ProjectImportProvider.addSteps(ProjectImportProvider.java:90)
at com.intellij.ide.util.newProjectWizard.modes.ImportMode.createSteps(ImportMode.java:75)
at com.intellij.ide.util.newProjectWizard.modes.WizardMode.getSteps(WizardMode.java:51)
at com.intellij.ide.util.newProjectWizard.AddModuleWizard.initModuleWizard(AddModuleWizard.java:140)
at com.intellij.ide.util.newProjectWizard.AddModuleWizard.(AddModuleWizard.java:97)
at com.intellij.ide.actions.ImportModuleAction.createImportWizard(ImportModuleAction.java:178)
at com.intellij.ide.actions.ImportModuleAction.selectFileAndCreateWizard(ImportModuleAction.java:122)
at com.intellij.ide.actions.ImportModuleAction.doImport(ImportModuleAction.java:61)
at com.intellij.ide.actions.ImportProjectAction.actionPerformed(ImportProjectAction.java:29)
at com.intellij.openapi.actionSystem.impl.ActionButton.actionPerformed(ActionButton.java:169)
at com.intellij.openapi.actionSystem.impl.ActionButton.performAction(ActionButton.java:132)
at com.intellij.openapi.actionSystem.impl.ActionButton.processMouseEvent(ActionButton.java:310)
at java.awt.Component.processEvent(Component.java:6298)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:673)
at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:494)
at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:333)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - IntelliJ IDEA 12.0.4 Build #IC-123.169
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - JDK: 1.8.0_111
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - VM: Java HotSpot(TM) 64-Bit Server VM
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - Vendor: Oracle Corporation
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - OS: Linux
[ 46767] ERROR - com.intellij.ide.IdeEventQueue - Last Action: WelcomeScreen.ImportProject

The mvn test-compile did complete successfully. but I am not sure I completed intelliJ set up.

Thank you again

Tagged:

Answers

  • so the intelliJ set up should be ran under the protected directory in gatk.

  • so the external example error is resolved after INTELLIJ is correctly importing the gatk-protected/protected subdirectory. CLOSED
    INFO] ------------------------------------------------------------------------
    [INFO] Reactor Summary:
    [INFO]
    [INFO] GATK Root ......................................... SUCCESS [0.773s]
    [INFO] GATK Aggregator ................................... SUCCESS [0.584s]
    [INFO] GATK GSALib ....................................... SUCCESS [0.516s]
    [INFO] GATK Utils ........................................ SUCCESS [4.854s]
    [INFO] GATK Engine ....................................... SUCCESS [2.437s]
    [INFO] GATK Tools Public ................................. SUCCESS [4.770s]
    [INFO] External Example .................................. SUCCESS [9.490s]
    [INFO] GATK Aggregator Public ............................ SUCCESS [0.010s]
    [INFO] GATK Tools Protected .............................. SUCCESS [3.646s]
    [INFO] GATK Package Distribution ......................... SUCCESS [15.302s]
    [INFO] GATK Aggregator Protected ......................... SUCCESS [0.009s]
    [INFO] ------------------------------------------------------------------------
    [INFO] BUILD SUCCESS
    [INFO] ------------------------------------------------------------------------
    [INFO] Total time: 42.657s
    [INFO] Finished at: Tue Jan 03 12:29:40 PST 2017
    [INFO] Final Memory: 52M/788M
    [INFO] -----------------------------------

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @arcolombo Can you clarify which instructions you're trying to follow? I don't recognize these steps.

  • arcolomboarcolombo LAMember
    edited January 2017

    First thank you for your response.

    I am trying to install GATK first and then muTect. muTect readMe suggests installing GATK first.

    so I did the following :

    1) clone gatk-protected

    2) set up the dev environment, setting up INTELLIJ and successfully running mvn compilations. the GATK is sourced. Note: I did not use git reset --hard 3.1 in my build.

    I've followed the intelliJ instructions here( http://gatkforums.broadinstitute.org/gatk/discussion/4023/setting-up-your-dev-environment-maven-and-intellij-for-gatk-3)
    arcolombo@arcolombo-ThinkPad-T450s:~/Documents/gatk-protected/target$ GenomeAnalysisTK.jar --help | head -40

    The Genome Analysis Toolkit (GATK) v3.7-0-g56f2c1a, Compiled 2017/01/03 21:25:04
    Copyright (c) 2010-2016 The Broad Institute
    For support and documentation go to https://software.broadinstitute.org/gatk
    [Tue Jan 03 13:41:17 PST 2017] Executing on Linux 4.4.0-57-generic amd64

    Java HotSpot(TM) 64-Bit Server VM 1.8.0_111-b14


    usage: java -jar GenomeAnalysisTK.jar -T [-args ] [-I ] [--showFullBamList] [-rbs
    ] [-rf ] [-drf ] [-L ] [-XL ] [-isr
    ] [-im ] [-ip ] [-R ] [-ndrs] [-maxRuntime
    ] [-maxRuntimeUnits ] [-dt ] [-dfrac ] [-dcov
    ] [-baq ] [-baqGOP ] [-fixNDN] [-fixMisencodedQuals]
    [-allowPotentiallyMisencodedQuals] [-OQ] [-DBQ ] [-PF ] [-BQSR ] [-qq
    ] [-SQQ ] [-DIQ] [-EOQ] [-preserveQ ]
    [-globalQScorePrior ] [-secondsBetweenProgressUpdates ] [-S
    ] [-rpr] [-kpr] [-sample_rename_mapping_file ] [-U ]
    [-disable_auto_index_creation_and_locking_when_reading_rods] [-no_cmdline_in_header] [-sites_only] [-writeFullFormat]
    [-compress ] [-simplifyBAM] [--disable_bam_indexing] [--generate_md5] [-nt ] [-nct
    ] [-mte] [-rgbl ] [-ped ] [-pedString
    ] [-pedValidationType ] [-variant_index_type ]
    [-variant_index_parameter ] [-ref_win_stop ] [-l ] [-log
    ] [-h] [-version]

    -T,--analysis_type Name of the tool to run
    -args,--arg_file Reads arguments from the
    specified file
    -I,--input_file Input file containing sequence
    data (BAM or CRAM)
    --showFullBamList Emit list of input BAM/CRAM
    files to log
    -rbs,--read_buffer_size Number of reads per SAM file
    to buffer in memory
    -rf,--read_filter Filters to apply to reads
    before analysis
    -drf,--disable_read_filter Read filters to disable
    -L,--intervals One or more genomic intervals
    over which to operate
    -XL,--excludeIntervals One or more genomic intervals
    to exclude from processing

    3) from a form post here, I simply download the muTect executable, and still can not run muTect using the pre-compiled .jar.

    arcolombo@arcolombo-ThinkPad-T450s:~/Downloads$ java -jar muTect-1.1.4.jar
    ERROR ------------------------------------------------------------------------------------------
    ERROR stack trace
    java.lang.ExceptionInInitializerError
    at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:160)
    at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:53)
    at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:56)
    at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)
    Caused by: java.lang.NullPointerException
    at org.reflections.Reflections.scan(Reflections.java:220)
    at org.reflections.Reflections.scan(Reflections.java:166)
    at org.reflections.Reflections.(Reflections.java:94)
    at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:77)
    ... 4 more
    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
    ERROR
    ERROR Please visit the wiki to see if this is a known problem
    ERROR If not, please post the error, with stack trace, to the GATK forum
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Code exception (see stack trace for error itself)
    ERROR ------------------------------------------------------------------------------------------
    arcolombo@arcolombo-ThinkPad-T450s:~/Downloads$

    4) if I try to compile me-self, I get errors for missing POMs

    mvn test-compile
    [INFO] Scanning for projects...
    [INFO]
    [INFO] ------------------------------------------------------------------------
    [INFO] Building Mutect 1.1.7
    [INFO] ------------------------------------------------------------------------
    [WARNING] The POM for org.broadinstitute.sting:gatk-protected:jar:3.1 is missing, no dependency information available
    [WARNING] The POM for org.broadinstitute.sting:gatk-framework:jar:tests:3.1 is missing, no dependency information available
    [INFO] ------------------------------------------------------------------------
    [INFO] BUILD FAILURE
    [INFO] ------------------------------------------------------------------------
    [INFO] Total time: 0.263 s
    [INFO] Finished at: 2017-01-03T13:45:00-08:00
    [INFO] Final Memory: 7M/117M
    [INFO] ------------------------------------------------------------------------
    [ERROR] Failed to execute goal on project mutect: Could not resolve dependencies for project org.broadinstitute.cga:mutect:jar:1.1.7: The following artifacts could not be resolved: org.broadinstitute.sting:gatk-protected:jar:3.1, org.broadinstitute.sting:gatk-framework:jar:tests:3.1: Failure to find org.broadinstitute.sting:gatk-protected:jar:3.1 in file:../../gatk-protected/public/repo was cached in the local repository, resolution will not be reattempted until the update interval of sting.public.repo.local has elapsed or updates are forced -> [Help 1]
    [ERROR]
    [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
    [ERROR] Re-run Maven using the -X switch to enable full debug logging.
    [ERROR]
    [ERROR] For more information about the errors and possible solutions, please read the following articles:
    [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

    Long story short I'm trying to either build muTect or use a source muTect

    questions:

    1) Where does my compiled Gatk.jar need to be in order for muTect to have cross-talk with the Gatk.jar ? I save the symbolic link into my /usr/local/bin and still no luck.

    2) Is mutect 1.1.7 compatible with GATK 3.7?

    thank you again

    AC

    Post edited by arcolombo on
  • i've also failed with compiling GATK using the reset hard 3.1. that will not compile GATK.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Oh I see. No, the old MuTect has not been updated to be compiled against versions of GATK later than 3.1. We provide a precompiled binary of MuTect 1.1.7 in the Downloads if that's all you need. Or you can try using the beta version of MuTect2, which is available within GATK 3.7.

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