Error I meet when install MuTect on a linux server

ttgumpttgump New JerseyMember
edited February 2017 in Ask the GATK team

Hi, I am trying to install MuTect on a linux server. By the instruction, I did the steps:

make a new source directory (e.g. mutect-src)
mkdir mutect-src
cd mutect-src

get MuTect source
git clone git@github.com:broadinstitute/mutect.git

get the GATK source and set to the latest tested version
git clone git@github.com:broadgsa/gatk-protected.git
cd gatk-protected
git reset --hard 3.1

build the GATK first and install it to the local mvn repo. Once GATK publishes to a public repo this will be much simpler
mvn -Ddisable.queue install

build MuTect and run unit tests (the target jar will be in target/mutect-*.jar)
cd ../mutect
mvn verify

run integration tests, if you like
./run_regression.pl
./tieout_regression.pl

It all successes until the step:mvn verify
Here is the error message:

[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: 0.343 s
[INFO] Finished at: 2017-02-16T17:24:18-08:00
[INFO] Final Memory: 24M/1963M
[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

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