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Compiling GATK from github

lindenblindenb FranceMember ✭✭

I'm trying to compile GATK from the github repo, using a new maven folder:

curl -kLo tmp.zip "https://github.com/broadgsa/gatk/archive/3.3.zip"
unzip tmp.zip
cd gatk-3.3/
/commun/data/packages/apache-maven-3.1.1/bin/mvn compile -Dmaven.repo.local=/commun/data/users/lindenb/tmp/GATK/m2

(...)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] GATK Root ......................................... SUCCESS [5.755s]
[INFO] GATK Aggregator ................................... SUCCESS [0.313s]
[INFO] GATK GSALib ....................................... SUCCESS [7.951s]
[INFO] GATK Utils ........................................ SUCCESS [16.481s]
[INFO] GATK Engine ....................................... SUCCESS [0.528s]
[INFO] GATK Tools Public ................................. SUCCESS [8.714s]
[INFO] External Example .................................. SUCCESS [2.401s]
[INFO] GATK Queue ........................................ SUCCESS [46.933s]
[INFO] GATK Queue Extensions Generator ................... SUCCESS [0.260s]
[INFO] GATK Queue Extensions Public ...................... FAILURE [0.930s]
[INFO] GATK Aggregator Public ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:31.050s
[INFO] Finished at: Fri Mar 13 10:06:42 CET 2015
[INFO] Final Memory: 49M/591M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project gatk-queue-extensions-public: Could not resolve dependencies for project org.broadinstitute.gatk:gatk-queue-extensions-public:jar:3.3: The following artifacts could not be resolved: org.broadinstitute.gatk:gatk-tools-public:jar:tests:3.3, org.broadinstitute.gatk:gatk-queue:jar:tests:3.3: Could not find artifact org.broadinstitute.gatk:gatk-tools-public:jar:tests:3.3 in gatk.public.repo.local (file:/commun/data/users/lindenb/tmp/GATK/gatk-3.3/public/gatk-queue-extensions-public/../../public/repo) -> [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
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :gatk-queue-extensions-public

I don't really understand the error message.
I understand that this GATK version only contains the public features but , am I wrong, I expect to find a jar 'GenomeAnalysisTK*'

How can I fix this ?

Thanks

Best Answers

Answers

  • lindenblindenb FranceMember ✭✭
    $ /commun/data/packages/apache-maven-3.1.1/bin/mvn clean -Dmaven.repo.local=/commun/data/users/lindenb/tmp/GATK/m2
    (...)
    $ /commun/data/packages/apache-maven-3.1.1/bin/mvn verify -Dmaven.repo.local=/commun/data/users/lindenb/tmp/GATK/m2
    
    [INFO] --- maven-sortpom-plugin:2.2:sort (default) @ gatk-aggregator-public ---
    [INFO] Sorting file /commun/data/users/lindenb/tmp/GATK/gatk-3.3/public/pom.xml
    [INFO] Pom file is already sorted, exiting
    [INFO] ------------------------------------------------------------------------
    [INFO] Reactor Summary:
    [INFO] 
    [INFO] GATK Root ......................................... SUCCESS [4.342s]
    [INFO] GATK Aggregator ................................... SUCCESS [1.983s]
    [INFO] GATK GSALib ....................................... SUCCESS [0.928s]
    [INFO] GATK Utils ........................................ SUCCESS [12.071s]
    [INFO] GATK Engine ....................................... SUCCESS [0.916s]
    [INFO] GATK Tools Public ................................. SUCCESS [30.725s]
    [INFO] External Example .................................. SUCCESS [15.306s]
    [INFO] GATK Queue ........................................ SUCCESS [57.429s]
    [INFO] GATK Queue Extensions Generator ................... SUCCESS [0.241s]
    [INFO] GATK Queue Extensions Public ...................... SUCCESS [55.205s]
    [INFO] GATK Aggregator Public ............................ SUCCESS [0.027s]
    [INFO] ------------------------------------------------------------------------
    [INFO] BUILD SUCCESS
    [INFO] ------------------------------------------------------------------------
    [INFO] Total time: 2:59.950s
    [INFO] Finished at: Fri Mar 13 12:03:30 CET 2015
    [INFO] Final Memory: 113M/1839M
    [INFO] ------------------------------------------------------------------------
    (...)
    
    

    Thank you , that's Better !

    But I cannot see any GenomeAnalysisTK*.jar or any executable jar

    $ find ./ -name "*.jar"
    ./public/external-example/target/original-external-example-1.0-SNAPSHOT.jar
    ./public/external-example/target/external-example-1.0-SNAPSHOT.jar
    ./public/gatk-engine/target/gatk-engine-3.3.jar
    ./public/gatk-engine/target/gatk-engine-3.3-tests.jar
    ./public/gatk-queue-extensions-generator/target/gatk-queue-extensions-generator-3.3.jar
    ./public/gatk-queue-extensions-public/target/gatk-queue-extensions-public-3.3.jar
    ./public/gatk-queue-extensions-public/target/gatk-queue-extensions-public-3.3-tests.jar
    ./public/gatk-queue/target/gatk-queue-3.3.jar
    ./public/gatk-queue/target/gatk-queue-3.3-tests.jar
    ./public/gatk-tools-public/target/gatk-tools-public-3.3.jar
    ./public/gatk-tools-public/target/gatk-tools-public-3.3-tests.jar
    ./public/gatk-utils/target/gatk-utils-3.3.jar
    ./public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
    ./public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar
    ./public/repo/picard/picard/1.120.1579/picard-1.120.1579.jar
    ./public/repo/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620.jar
    
    
    $ find ./public/gatk-* -name "*.jar" | while read F; do java -jar ${F} ; done
    no main manifest attribute, in ./public/gatk-engine/target/gatk-engine-3.3.jar
    no main manifest attribute, in ./public/gatk-engine/target/gatk-engine-3.3-tests.jar
    no main manifest attribute, in ./public/gatk-queue/target/gatk-queue-3.3.jar
    no main manifest attribute, in ./public/gatk-queue/target/gatk-queue-3.3-tests.jar
    no main manifest attribute, in ./public/gatk-queue-extensions-generator/target/gatk-queue-extensions-generator-3.3.jar
    no main manifest attribute, in ./public/gatk-queue-extensions-public/target/gatk-queue-extensions-public-3.3.jar
    no main manifest attribute, in ./public/gatk-queue-extensions-public/target/gatk-queue-extensions-public-3.3-tests.jar
    no main manifest attribute, in ./public/gatk-tools-public/target/gatk-tools-public-3.3.jar
    no main manifest attribute, in ./public/gatk-tools-public/target/gatk-tools-public-3.3-tests.jar
    no main manifest attribute, in ./public/gatk-utils/target/gatk-utils-3.3.jar
    
  • lindenblindenb FranceMember ✭✭

    got it, thanks.

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