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Use GATK R Library (gsalib), how to build?

qyuqyu Member
edited January 2013 in Ask the GATK team

Hi,

Does anyone use GATK R Library (gsalib)? I follow the guide at this link (http://gatkforums.broadinstitute.org/discussion/1244/what-is-a-gatkreport), when I type "ant gsalib" in my linux system with Java 1.6, the building failed. Here is the error message.

5:00pm qyu@vbronze /bit/data01/projects/prod_scripts/GATK/gatk-master $ ant gsalib Buildfile: build.xml

BUILD FAILED /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml:184: The type doesn't support the "erroronmissingdir" attribute.

Can anyone know what is wrong here?

Many thanks,
Qing

Post edited by Geraldine_VdAuwera on
Tagged:

Answers

  • Thanks! Now I use ant-1.8, but I get a different error message as below. I have granted full writing permission to the working directory and files.

    10:37am qyu@vbronze /bit/data01/projects/prod_scripts/GATK/gatk-master $ ant gsalib
    Buildfile: /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml

    gsalib:
    [exec] * installing to library â
    [exec] Error: ERROR: no permission to install to directory â

    BUILD FAILED
    /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml:1039: exec returned: 1

    Total time: 3 seconds

    Can you find what is wrong here?

    Many thanks,
    Qing

  • No, I can't help there. I would try to figure out how it got the name of the directory to install to, and why it's such a funny name. It may just be a bad environment variable or something

  • Thank you very much!

  • sudo ant gsalib
    Buildfile: gatk-master/build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    gsalib:
    [exec] * installing to library ‘/usr/lib64/R/library’
    [exec] * installing source package ‘gsalib’ ...
    [exec] ERROR: a 'NAMESPACE' file is required
    [exec] * removing ‘/usr/lib64/R/library/gsalib’

    BUILD FAILED

    How to reslove?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Can you try doing a full build (ant clean dist) and see if that works?

    Also, what version of the source are you using?

  • ant clean dist->ant gsalib,It's showed the same problem.Download from https://github.com/broadgsa/gatk.This version as follow:
    Java:1.6._43,Ant:1.8.4,gatk:2.4.9.

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @hong_010, please see this post for a solution contributed by a user who had the same problem: http://gatkforums.broadinstitute.org/discussion/comment/5130#Comment_5130

  • Hi,my problem isnot the same with @ying_sheng_1.Because when I run the ant clean dist ,there was the phenomenon:

    Buildfile: gatk-master/build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    I can not resolve it.Would you give me a help?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    The cloverlib.xml is not a blocking error, it probably has nothing to do with your build failure. Can you post the complete console output that you get when you run ant clean dist?

  • hong_010hong_010 Member
    edited April 2013

    $ ant clean dist

    Buildfile: gatk-master/build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    clean.javadoc:

    clean.scaladoc:

    clean.gatkdocs:

    -check.clover:

    clean.clover:

    clean:
    [delete] Deleting directory gatk-master/build
    [delete] Deleting directory gatk-master/lib
    [delete] Deleting directory gatk-master/dist

    git.describe:
    [exec] Result: 128

    tagged.build.version:

    git.rev-parse:
    [exec] Result: 128

    untagged.build.version:

    generate.build.version:

    init:
    [echo] BUILD PROPERTIES
    [echo] Include Scala? : yes
    [echo] Include Private? : no
    [echo] Include Protected? : no
    [echo] Include External? : no
    [echo] Include Contracts? : no
    [echo] Source revision : exported
    [echo] Build time : 2013/04/13 16:42:46
    [mkdir] Created dir: gatk-master/build
    [mkdir] Created dir: gatk-master/lib
    [mkdir] Created dir: gatk-master/build/java/classes
    [mkdir] Created dir: gatk-master/build/java/contracts

    init.resolve:
    [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
    [get] To: /home/yangch/.ant/lib/ivy-2.2.0.jar
    [get] Not modified - so not downloaded
    [get] Getting: http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/2.1.3/maven-ant-tasks-2.1.3.jar
    [get] To: /home/yangch/.ant/lib/maven-ant-tasks-2.1.3.jar
    [get] Not modified - so not downloaded

    resolve:
    [ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ ::
    [ivy:retrieve] :: loading settings :: file = gatk-master/settings/ivysettings.xml
    [ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;working@master
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] found net.sf#sam;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] net.sf#sam;latest.integration
    [ivy:retrieve] found net.sf#picard;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] net.sf#picard;latest.integration
    [ivy:retrieve] found edu.mit.broad#picard-private-parts;2662 in projects
    [ivy:retrieve] [2662] edu.mit.broad#picard-private-parts;latest.integration
    [ivy:retrieve] found org.broad#tribble;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] org.broad#tribble;latest.integration
    [ivy:retrieve] found org.broadinstitute#variant;1.85.1357 in projects
    [ivy:retrieve] [1.85.1357] org.broadinstitute#variant;latest.integration
    [ivy:retrieve] found log4j#log4j;1.2.15 in maven
    [ivy:retrieve] found javax.mail#mail;1.4.4 in maven
    [ivy:retrieve] found javax.activation#activation;1.1 in maven
    [ivy:retrieve] found colt#colt;1.2.0 in maven
    [ivy:retrieve] found concurrent#concurrent;1.3.4 in maven
    [ivy:retrieve] found org.simpleframework#simple-xml;2.0.4 in maven
    [ivy:retrieve] found stax#stax-api;1.0.1 in maven
    [ivy:retrieve] found stax#stax;1.2.0 in maven
    [ivy:retrieve] found org.apache.bcel#bcel;5.2 in maven
    [ivy:retrieve] found jakarta-regexp#jakarta-regexp;1.4 in maven
    [ivy:retrieve] found org.reflections#reflections;0.9.8 in maven
    [ivy:retrieve] found com.google.guava#guava;11.0.2 in maven
    [ivy:retrieve] found com.google.code.findbugs#jsr305;1.3.9 in maven
    [ivy:retrieve] found javassist#javassist;3.12.1.GA in maven
    [ivy:retrieve] found dom4j#dom4j;1.6.1 in maven
    [ivy:retrieve] found xml-apis#xml-apis;1.0.b2 in maven
    [ivy:retrieve] found org.slf4j#slf4j-log4j12;1.6.1 in maven
    [ivy:retrieve] found org.slf4j#slf4j-api;1.6.1 in maven
    [ivy:retrieve] found log4j#log4j;1.2.16 in maven
    [ivy:retrieve] found gov.nist#Jama;1.0.2 in projects
    [ivy:retrieve] found net.sf.jgrapht#jgrapht;0.8.3 in maven
    [ivy:retrieve] found org.freemarker#freemarker;2.3.18 in maven
    [ivy:retrieve] found org.apache.commons#commons-email;1.2 in maven
    [ivy:retrieve] found org.apache.commons#commons-jexl;2.1.1 in maven
    [ivy:retrieve] found commons-logging#commons-logging;1.1.1 in maven
    [ivy:retrieve] found commons-lang#commons-lang;2.5 in maven
    [ivy:retrieve] found commons-io#commons-io;2.1 in maven
    [ivy:retrieve] found commons-collections#commons-collections;3.2.1 in maven
    [ivy:retrieve] found org.apache.commons#commons-math;2.2 in maven
    [ivy:retrieve] found net.java.dev.jna#jna;3.2.7 in maven
    [ivy:retrieve] found net.java.dev.jets3t#jets3t;0.8.1 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.3 in maven
    [ivy:retrieve] found commons-httpclient#commons-httpclient;3.1 in maven
    [ivy:retrieve] found com.jamesmurty.utils#java-xmlbuilder;0.4 in maven
    [ivy:retrieve] found net.sf.gridscheduler#drmaa;6.2u5p2 in projects
    [ivy:retrieve] [6.2u5p2] net.sf.gridscheduler#drmaa;latest.integration
    [ivy:retrieve] found org.scala-lang#scala-compiler;2.9.2 in maven
    [ivy:retrieve] found org.scala-lang#scala-library;2.9.2 in maven
    [ivy:retrieve] found org.testng#testng;6.8 in maven
    [ivy:retrieve] found junit#junit;4.10 in maven
    [ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in maven
    [ivy:retrieve] found org.beanshell#bsh;2.0b4 in maven
    [ivy:retrieve] found com.beust#jcommander;1.27 in maven
    [ivy:retrieve] found org.yaml#snakeyaml;1.6 in maven
    [ivy:retrieve] found org.uncommons#reportng;1.1.2 in maven
    [ivy:retrieve] found velocity#velocity;1.4 in maven
    [ivy:retrieve] found velocity#velocity-dep;1.4 in maven
    [ivy:retrieve] found com.google.caliper#caliper;0.5-rc1 in maven
    [ivy:retrieve] found com.google.code.java-allocation-instrumenter#java-allocation-instrumenter;2.0 in maven
    [ivy:retrieve] found asm#asm;3.3.1 in maven
    [ivy:retrieve] found asm#asm-analysis;3.3.1 in maven
    [ivy:retrieve] found asm#asm-tree;3.3.1 in maven
    [ivy:retrieve] found asm#asm-commons;3.3.1 in maven
    [ivy:retrieve] found asm#asm-util;3.3.1 in maven
    [ivy:retrieve] found asm#asm-xml;3.3.1 in maven
    [ivy:retrieve] found com.google.inject#guice;3.0 in maven
    [ivy:retrieve] found javax.inject#javax.inject;1 in maven
    [ivy:retrieve] found aopalliance#aopalliance;1.0 in maven
    [ivy:retrieve] found org.sonatype.sisu.inject#cglib;2.2.1-v20090111 in maven
    [ivy:retrieve] found com.google.code.cofoja#cofoja;1.0-r139 in projects
    [ivy:retrieve] found asm#asm-all;3.3.1 in maven
    [ivy:retrieve] found org.apache.poi#poi;3.8-beta3 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.5 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml-schemas;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.xmlbeans#xmlbeans;2.3.0 in maven
    [ivy:retrieve] found net.sf.snpeff#snpeff;2.0.5 in projects
    [ivy:retrieve] found org.mongodb#mongo-java-driver;2.7.3 in maven
    [ivy:retrieve] found com.google.code.gson#gson;2.2.2 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpclient;4.1.1 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpcore;4.1 in maven
    [ivy:retrieve] :: resolution report :: resolve 6413ms :: artifacts dl 51ms
    [ivy:retrieve] :: evicted modules:
    [ivy:retrieve] log4j#log4j;1.2.15 by [log4j#log4j;1.2.16] in [default]
    [ivy:retrieve] javax.mail#mail;1.4 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] javax.mail#mail;1.4.1 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.3 by [commons-codec#commons-codec;1.5] in [default]
    [ivy:retrieve] org.testng#testng;5.0 by [org.testng#testng;6.8] in [default]
    [ivy:retrieve] com.google.code.gson#gson;1.7.1 by [com.google.code.gson#gson;2.2.2] in [default]
    [ivy:retrieve] com.google.guava#guava;11.0.1 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] com.google.guava#guava;r08 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] asm#asm;3.1 by [asm#asm;3.3.1] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.4 by [commons-codec#commons-codec;1.5] in [default]
    ---------------------------------------------------------------------
    | | modules || artifacts |
    | conf | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    | default | 83 | 6 | 0 | 10 || 73 | 0 |
    ---------------------------------------------------------------------
    [ivy:retrieve] :: retrieving :: org.broadinstitute#Sting
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] 73 artifacts copied, 0 already retrieved (52083kB/378ms)

    gatk.compile.internal.source:
    [javac] Compiling 659 source files to gatk-master/build/java/classes
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/refdata/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/commandline/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/walkers/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/filters/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/queue/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/providers/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/alignment/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/threading/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reference/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/executive/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/sam/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/traversals/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/rmd/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/gatk/iterators/package-info.class
    [javac] Creating empty gatk-master/build/java/classes/org/broadinstitute/sting/utils/fasta/package-info.class

    gatk.compile.external.source:

    gatk.compile.source:

    gatk.contracts:

    gatk.compile:

    init.extracthelp:
    [loadfile] gatk-master/build/java/classes/StingText.properties doesn't exist

    extracthelp:
    [javadoc] Generating Javadoc
    [javadoc] Javadoc execution

    init.queue-extensions.generate:

    queue-extensions.generate:
    [mkdir] Created dir: gatk-master/build/queue-extensions/src
    [echo] Generating Queue GATK extensions...

    init.scala.compile:

    scala.compile:
    [mkdir] Created dir: gatk-master/build/scala/classes
    [echo] Building Scala...
    [scalac] Compiling 101 source files to gatk-master/build/scala/classes
    [scalac] Compiling 90 source files to gatk-master/build/scala/classes

    sting.compile:

    init.jar:
    [mkdir] Created dir: gatk-master/dist
    [copy] Copying 73 files to gatk-master/dist

    R.public.tar:
    [mkdir] Created dir: gatk-master/build/R/src/org/broadinstitute/sting/utils/R
    [tar] Nothing to do: gatk-master/build/R/src/org/broadinstitute/sting/utils/R/gsalib.tar.gz is up to date.

    R.script.stage:
    [mkdir] Created dir: gatk-master/build/R/stage
    [copy] Copying 3 files to gatk-master/build/R/stage

    sting-utils.jar:
    [jar] Building jar: gatk-master/dist/StingUtils.jar

    gatk.jar:
    [jar] Building jar: gatk-master/dist/GenomeAnalysisTK.jar
    [jar] Building jar: gatk-master/dist/Aligner.jar
    [subant] No sub-builds to iterate on

    queue.jar:
    [jar] Building jar: gatk-master/dist/Queue.jar

    sting.jar:

    init.manifests:

    sting-utils.manifests:
    [jar] Updating jar: gatk-master/dist/StingUtils.jar

    gatk.manifests:
    [jar] Updating jar: gatk-master/dist/GenomeAnalysisTK.jar

    queue.manifests:
    [jar] Updating jar: gatk-master/dist/Queue.jar

    sting.manifests:

    dist:

    BUILD SUCCESSFUL
    Total time: 1 minute 17 seconds

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Great, your build is successful! Then you just need to do the same steps as Ying Sheng, either install gsalib manually or fix the namespace issue as Ying Sheng described.

  • Hi!
    My build was successful,but it pointed out:

    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    When I installed gaslib,it pointed out:

    $ ls -l public/R/src/org/broadinstitute/sting/utils/R/
    total 128
    drwxr-xr-x 5 yang bio 131072 Mar 19 13:09 gsalib

    $ R CMD INSTALL public/R/src/org/broadinstitute/sting/utils/R/
    Warning: invalid package ‘public/R/src/org/broadinstitute/sting/utils/R/’
    Error: ERROR: no packages specified

    Why?

    Would you give me a help?

    Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Hong,

    The cloverlib error is not important, don't worry about it.

    For the install command, you have to add "gsalib" to the package path. You're passing the actual package, not the enclosing directory that it is in.

  • hong_010hong_010 Member
    edited April 2013

    Thank you very much!

    I have done the following modifications:

    1.cd public/R/src/org/broadinstitute/sting/utils/R/gsalib --> create the NAMESPACE file

    2.R CMD INSTALL -l R_library gatk-master/public/R/src/org/broadinstitute/sting/utils/R/gsalib

    It works now!

    The most important thing is to set the installation directory。

    I hope to be useful to others。

    ref:http://stackoverflow.com/questions/8012596/error-with-asreml-d-package-in-r-2-14-0/8014357#8014357

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Thanks for reporting your full solution! I'm sure this will be helpful for other users.

  • hi,
    i have the following problem. I have download the gatk-master.zip file from Github.
    Using the ant clean dist command produces an error -> Build failed.

    Here are the console output:

    [root@radjedef gatk-master]# ant clean dist
    Buildfile: build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    clean.javadoc:

    clean.scaladoc:

    clean.gatkdocs:

    -check.clover:

    clean.clover:

    clean:
    [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/build
    [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/lib
    [delete] Deleting directory /export/vols/meritites_v2/programs/GATK/gatk-master/dist

    git.describe:
    [exec] Result: 128

    tagged.build.version:

    git.rev-parse:
    [exec] Result: 128

    untagged.build.version:

    generate.build.version:

    init:
    [echo] BUILD PROPERTIES
    [echo] Include Scala? : yes
    [echo] Include Private? : no
    [echo] Include Protected? : no
    [echo] Include External? : no
    [echo] Include Contracts? : no
    [echo] Source revision : exported
    [echo] Build time : 2013/04/18 13:40:33
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/lib
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/contracts

    init.resolve:
    [get] Getting: http://repo1.maven.org/maven2/org/apache/ivy/ivy/2.2.0/ivy-2.2.0.jar
    [get] To: /root/.ant/lib/ivy-2.2.0.jar
    [get] Not modified - so not downloaded
    [get] Getting: http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/2.1.3/maven-ant-tasks-2.1.3.jar
    [get] To: /root/.ant/lib/maven-ant-tasks-2.1.3.jar
    [get] Not modified - so not downloaded

    resolve:
    [ivy:retrieve] :: Ivy 2.2.0 - 20100923230623 :: http://ant.apache.org/ivy/ ::
    [ivy:retrieve] :: loading settings :: file = /export/vols/meritites_v2/programs/GATK/gatk-master/settings/ivysettings.xml
    [ivy:retrieve] :: resolving dependencies :: org.broadinstitute#Sting;working@localhost
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] found net.sf#sam;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] net.sf#sam;latest.integration
    [ivy:retrieve] found net.sf#picard;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] net.sf#picard;latest.integration
    [ivy:retrieve] found edu.mit.broad#picard-private-parts;2662 in projects
    [ivy:retrieve] [2662] edu.mit.broad#picard-private-parts;latest.integration
    [ivy:retrieve] found org.broad#tribble;1.84.1337 in projects
    [ivy:retrieve] [1.84.1337] org.broad#tribble;latest.integration
    [ivy:retrieve] found org.broadinstitute#variant;1.85.1357 in projects
    [ivy:retrieve] [1.85.1357] org.broadinstitute#variant;latest.integration
    [ivy:retrieve] found log4j#log4j;1.2.15 in maven
    [ivy:retrieve] found javax.mail#mail;1.4.4 in maven
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    [ivy:retrieve] found colt#colt;1.2.0 in maven
    [ivy:retrieve] found concurrent#concurrent;1.3.4 in maven
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    [ivy:retrieve] found stax#stax-api;1.0.1 in maven
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    [ivy:retrieve] found jakarta-regexp#jakarta-regexp;1.4 in maven
    [ivy:retrieve] found org.reflections#reflections;0.9.8 in maven
    [ivy:retrieve] found com.google.guava#guava;11.0.2 in maven
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    [ivy:retrieve] found javassist#javassist;3.12.1.GA in maven
    [ivy:retrieve] found dom4j#dom4j;1.6.1 in maven
    [ivy:retrieve] found xml-apis#xml-apis;1.0.b2 in maven
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    [ivy:retrieve] found log4j#log4j;1.2.16 in maven
    [ivy:retrieve] found gov.nist#Jama;1.0.2 in projects
    [ivy:retrieve] found net.sf.jgrapht#jgrapht;0.8.3 in maven
    [ivy:retrieve] found org.freemarker#freemarker;2.3.18 in maven
    [ivy:retrieve] found org.apache.commons#commons-email;1.2 in maven
    [ivy:retrieve] found org.apache.commons#commons-jexl;2.1.1 in maven
    [ivy:retrieve] found commons-logging#commons-logging;1.1.1 in maven
    [ivy:retrieve] found commons-lang#commons-lang;2.5 in maven
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    [ivy:retrieve] found org.apache.commons#commons-math;2.2 in maven
    [ivy:retrieve] found net.java.dev.jna#jna;3.2.7 in maven
    [ivy:retrieve] found net.java.dev.jets3t#jets3t;0.8.1 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.3 in maven
    [ivy:retrieve] found commons-httpclient#commons-httpclient;3.1 in maven
    [ivy:retrieve] found com.jamesmurty.utils#java-xmlbuilder;0.4 in maven
    [ivy:retrieve] found net.sf.gridscheduler#drmaa;6.2u5p2 in projects
    [ivy:retrieve] [6.2u5p2] net.sf.gridscheduler#drmaa;latest.integration
    [ivy:retrieve] found org.scala-lang#scala-compiler;2.9.2 in maven
    [ivy:retrieve] found org.scala-lang#scala-library;2.9.2 in maven
    [ivy:retrieve] found org.testng#testng;6.8 in maven
    [ivy:retrieve] found junit#junit;4.10 in maven
    [ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in maven
    [ivy:retrieve] found org.beanshell#bsh;2.0b4 in maven
    [ivy:retrieve] found com.beust#jcommander;1.27 in maven
    [ivy:retrieve] found org.yaml#snakeyaml;1.6 in maven
    [ivy:retrieve] found org.uncommons#reportng;1.1.2 in maven
    [ivy:retrieve] found velocity#velocity;1.4 in maven
    [ivy:retrieve] found velocity#velocity-dep;1.4 in maven
    [ivy:retrieve] found com.google.caliper#caliper;0.5-rc1 in maven
    [ivy:retrieve] found com.google.code.java-allocation-instrumenter#java-allocation-instrumenter;2.0 in maven
    [ivy:retrieve] found asm#asm;3.3.1 in maven
    [ivy:retrieve] found asm#asm-analysis;3.3.1 in maven
    [ivy:retrieve] found asm#asm-tree;3.3.1 in maven
    [ivy:retrieve] found asm#asm-commons;3.3.1 in maven
    [ivy:retrieve] found asm#asm-util;3.3.1 in maven
    [ivy:retrieve] found asm#asm-xml;3.3.1 in maven
    [ivy:retrieve] found com.google.inject#guice;3.0 in maven
    [ivy:retrieve] found javax.inject#javax.inject;1 in maven
    [ivy:retrieve] found aopalliance#aopalliance;1.0 in maven
    [ivy:retrieve] found org.sonatype.sisu.inject#cglib;2.2.1-v20090111 in maven
    [ivy:retrieve] found com.google.code.cofoja#cofoja;1.0-r139 in projects
    [ivy:retrieve] found asm#asm-all;3.3.1 in maven
    [ivy:retrieve] found org.apache.poi#poi;3.8-beta3 in maven
    [ivy:retrieve] found commons-codec#commons-codec;1.5 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.poi#poi-ooxml-schemas;3.8-beta3 in maven
    [ivy:retrieve] found org.apache.xmlbeans#xmlbeans;2.3.0 in maven
    [ivy:retrieve] found net.sf.snpeff#snpeff;2.0.5 in projects
    [ivy:retrieve] found org.mongodb#mongo-java-driver;2.7.3 in maven
    [ivy:retrieve] found com.google.code.gson#gson;2.2.2 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpclient;4.1.1 in maven
    [ivy:retrieve] found org.apache.httpcomponents#httpcore;4.1 in maven
    [ivy:retrieve] :: resolution report :: resolve 5507ms :: artifacts dl 80ms
    [ivy:retrieve] :: evicted modules:
    [ivy:retrieve] log4j#log4j;1.2.15 by [log4j#log4j;1.2.16] in [default]
    [ivy:retrieve] javax.mail#mail;1.4 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] javax.mail#mail;1.4.1 by [javax.mail#mail;1.4.4] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.3 by [commons-codec#commons-codec;1.5] in [default]
    [ivy:retrieve] org.testng#testng;5.0 by [org.testng#testng;6.8] in [default]
    [ivy:retrieve] com.google.code.gson#gson;1.7.1 by [com.google.code.gson#gson;2.2.2] in [default]
    [ivy:retrieve] com.google.guava#guava;11.0.1 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] com.google.guava#guava;r08 by [com.google.guava#guava;11.0.2] in [default]
    [ivy:retrieve] asm#asm;3.1 by [asm#asm;3.3.1] in [default]
    [ivy:retrieve] commons-codec#commons-codec;1.4 by [commons-codec#commons-codec;1.5] in [default]
    ---------------------------------------------------------------------
    | | modules || artifacts |
    | conf | number| search|dwnlded|evicted|| number|dwnlded|
    ---------------------------------------------------------------------
    | default | 83 | 6 | 0 | 10 || 73 | 0 |
    ---------------------------------------------------------------------
    [ivy:retrieve] :: retrieving :: org.broadinstitute#Sting
    [ivy:retrieve] confs: [default]
    [ivy:retrieve] 73 artifacts copied, 0 already retrieved (52083kB/513ms)

    gatk.compile.internal.source:
    [javac] Compiling 659 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/refdata/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/commandline/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/walkers/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/filters/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/queue/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/providers/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/alignment/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/threading/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reference/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/executive/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/sam/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/traversals/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/rmd/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/datasources/reads/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/gatk/iterators/package-info.class
    [javac] Creating empty /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/org/broadinstitute/sting/utils/fasta/package-info.class

    gatk.compile.external.source:

    gatk.compile.source:

    gatk.contracts:

    gatk.compile:

    init.extracthelp:
    [loadfile] /export/vols/meritites_v2/programs/GATK/gatk-master/build/java/classes/StingText.properties doesn't exist

    extracthelp:
    [javadoc] Generating Javadoc
    [javadoc] Javadoc execution

    init.queue-extensions.generate:

    queue-extensions.generate:
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/queue-extensions/src
    [echo] Generating Queue GATK extensions...

    init.scala.compile:

    scala.compile:
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes
    [echo] Building Scala...
    [scalac] Compiling 101 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes
    [scalac] Compiling 90 source files to /export/vols/meritites_v2/programs/GATK/gatk-master/build/scala/classes

    sting.compile:

    init.jar:
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/dist
    [copy] Copying 73 files to /export/vols/meritites_v2/programs/GATK/gatk-master/dist

    R.public.tar:
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/src/org/broadinstitute/sting/utils/R
    [tar] Building tar: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/src/org/broadinstitute/sting/utils/R/gsalib.tar.gz

    R.script.stage:
    [mkdir] Created dir: /export/vols/meritites_v2/programs/GATK/gatk-master/build/R/stage

    BUILD FAILED
    /export/vols/meritites_v2/programs/GATK/gatk-master/build.xml:643: No supported regular expression matcher found: java.lang.ClassNotFoundException: org.apache.tools.ant.util.regexp.Jdk14RegexpMatcher

    Total time: 1 minute 29 seconds

    Thanks for help!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    This looks like an environment issue. What is your platform and java / JDK version?

  • droazendroazen Cambridge, MADev

    It's probably your ant version -- you should be using ant 1.7 or 1.8.

  • CarolCarol Member

    I have got problem in installing gsalib

    ant gsalib
    Buildfile: /home/carol/NGS/pgm/GenomeAnalysisTK-2.5-2-gf57256b/gatk-master/build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    gsalib:
    [exec] * installing to library ‘/home/carol/R/x86_64-pc-linux-gnu-library/3.0’
    [exec] * installing source package ‘gsalib’ ...
    [exec] ERROR: a 'NAMESPACE' file is required
    [exec] * removing ‘/home/carol/R/x86_64-pc-linux-gnu-library/3.0/gsalib’

    BUILD FAILED
    /home/carol/NGS/pgm/GenomeAnalysisTK-2.5-2-gf57256b/gatk-master/build.xml:1061: exec returned: 1

    I used ant clean dist but doesn't help. where should git be located?

    ant clean dist
    Buildfile: /home/carol/NGS/pgm/GenomeAnalysisTK-2.5-2-gf57256b/gatk-master/build.xml
    [taskdef] Could not load definitions from resource cloverlib.xml. It could not be found.

    clean.javadoc:

    clean.scaladoc:

    clean.gatkdocs:

    -check.clover:

    clean.clover:

    clean:

    git.describe:

    BUILD FAILED
    /home/carol/NGS/pgm/GenomeAnalysisTK-2.5-2-gf57256b/gatk-master/build.xml:309: Execute failed: java.io.IOException: Cannot run program "git": error=2, No such file or directory
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1042)
    at java.lang.Runtime.exec(Runtime.java:615)
    at org.apache.tools.ant.taskdefs.Execute$Java13CommandLauncher.exec(Execute.java:862)
    at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:481)
    at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:495)
    at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:631)
    at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672)
    at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498)
    at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
    at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
    at org.apache.tools.ant.Task.perform(Task.java:348)
    at org.apache.tools.ant.Target.execute(Target.java:390)
    at org.apache.tools.ant.Target.performTasks(Target.java:411)
    at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
    at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
    at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
    at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
    at org.apache.tools.ant.Main.runBuild(Main.java:809)
    at org.apache.tools.ant.Main.startAnt(Main.java:217)
    at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
    at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
    Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.(UNIXProcess.java:135)
    at java.lang.ProcessImpl.start(ProcessImpl.java:130)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1023)
    ... 23 more

    Total time: 0 seconds

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    edited June 2013

    Hi Carol,

    Please read the earlier posts in this thread; especially @hong_010's post, which gives a simple solution to your problem.

  • CarolCarol Member

    Thanks Geraldine. It works!

    where is it possible to have the description of columns header in the report file? It's possible to find some few on your web site but they are not complete (all columns header).

    Many thanks,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Carol,

    We don't provide complete descriptions of the report tables / columns because they depend on which tools are used (e.g. BaseRecalibrator generates different content compared to VariantRecalibrator, etc) and they can change between versions too. Usually the column names are self-explanatory. If you run into any specific ones that you don't understand, feel free to post them along with a brief description of where they come from.

  • CarolCarol Member

    For the columns header, I had referred to the variantEval output or report.

    If I understood correctly, variantEval generates statistics results on variants but doesn't specify the variants what they are, at which loci they occur, the type of variant (missense etc) and other specific info rather than overall statistics. If so, is there any way to extract these types of specific info?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That's right, VariantEval produces statistics that describe various properties of the callset, rather than individual sites. The "specific info" is contained in the VCF file, and there are various ways to access that information, but it depends what you want to do with it.

  • @qyu said:
    Hi,

    Does anyone use GATK R Library (gsalib)? I follow the guide at this link (http://gatkforums.broadinstitute.org/discussion/1244/what-is-a-gatkreport), when I type "ant gsalib" in my linux system with Java 1.6, the building failed. Here is the error message.

    5:00pm qyu@vbronze /bit/data01/projects/prod_scripts/GATK/gatk-master $ ant gsalib Buildfile: build.xml

    BUILD FAILED /bit/data01/projects/prod_scripts/GATK/gatk-master/build.xml:184: The type doesn't support the "erroronmissingdir" attribute.

    Can anyone know what is wrong here?

    Many thanks,
    Qing

    how do you solve you problem? I meet it like it. I can not solve it ?Can you give some advice?
    Thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    If you can't build using ant (maybe due to a version problem, you can try installing the R library directly (this is what the ant command does anyway), following the advice given earlier in this thread by hong_10. Basically you do

    1.cd public/R/src/org/broadinstitute/sting/utils/R/gsalib --> create the NAMESPACE file

    1. R CMD INSTALL -l R_library gatk-master/public/R/src/org/broadinstitute/sting/utils/R/gsalib

    We are in the process of rewriting gsalib so that it can be put in CRAN, which will make all these problems go away.

  • @Geraldine_VdAuwera said:
    If you can't build using ant (maybe due to a version problem, you can try installing the R library directly (this is what the ant command does anyway), following the advice given earlier in this thread by hong_10. Basically you do

    1.cd public/R/src/org/broadinstitute/sting/utils/R/gsalib --> create the NAMESPACE file

    1. R CMD INSTALL -l R_library gatk-master/public/R/src/org/broadinstitute/sting/utils/R/gsalib

    We are in the process of rewriting gsalib so that it can be put in CRAN, which will make all these problems go away.

    many Thanks, it seems worked, but when I type in R,it print:

    library(gsalib) ## seems no error
    d=gsa.read.gatkreport("DataProcessing-gatk.grp")

    Error: could not find function "gsa.read.gatkreport"

    I do not know why?
    many thanks.

  • many Thanks, it seems worked, but when I type in R,it print:

    library(gsalib) ## seems no error
    d=gsa.read.gatkreport("DataProcessing-gatk.grp")
    Error: could not find function "gsa.read.gatkreport"

    I do not know why?
    many thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hmm, that is strange. What version of GATK are you using?

  • wangl0807wangl0807 Member
    edited June 2013

    Many thanks for your reply,I use GenomeAnalysisTK-2.5-2-gf57256b,Now it seems work:

    library(gsalib)
    d = gsa.read.gatkreport("/GATK/snp/Lib1-realn-confidence-1.grp")
    summary(d)

    Length Class Mode
    Arguments 2 data.frame list
    Quantized 3 data.frame list
    RecalTable0 6 data.frame list
    RecalTable1 6 data.frame list
    RecalTable2 8 data.frame list

    but when I use ' -plots Lib1-post-recal.grp.pdf ',there is no pdf , I have install R packages as other friends said in this forum . I use -l DEBUG, it print ' DEBUG 23:59:45,015 GATKRunReport - A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is Run statistics report upload to AWS S3 timed-out ',
    error in there, I place GenomeAnalysisTK-2.5-2 and gatk-master in different directory, I don't know how to set path? Should I set path?
    or any other errors in there?
    many tahnks .

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That error should not affect the plotting, it is unrelated and does not interrupt the rest of the program run.

    Can you please post the complete output that you get from the recalibration run?

  • Thanks. Yes, you are right. I just set R environment path, Now ,it work, I am a little doubt, Do I must load the .grpfile into R before I want to plot everary time?
    many thanks to you.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    No, the program should automatically load it for you and make the plots when you run it.

  • edited August 2014

    I forgot to mention in my previous post that using CRAN did not work for me - is gsalib maybe not yet mirrored to all repos available when trying to install from within R?

    referring to:
    http://www.broadinstitute.org/gatk/guide/tagged?tag=gsalib

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @philipp_henrich Can you clarify what you mean by that? Did you get an error message from CRAN?

  • Hi Geraldine, the error was about that gsalib was not found. I selected a CRAN server from France, Montpellier. Same when I repeated one day later (from a different, non-firewalled network, if that matters). The US server(s) worked fine and my pipeline is up an running again. Thanks for the excellent work on the speed improvement in v3+, this helps a lot since NGS data is just coming in continuously.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That's odd, I'm not sure why that would be the case. I'll ask the CRAN maintainers if there is something they can do one their end.

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