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gatk-3.8/settings/ivysettings.xml

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Move to ivy for dependency management. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@31 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 01:14:04 +08:00
<ivysettings>
<properties file="${ivy.settings.dir}/ivysettings.properties"/>
<settings defaultResolver="libraries"/>
<resolvers>
<filesystem name="projects">
<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
</filesystem>
Changed logging level to default at INFO instead of WARN. Changes to StingUtils command line for use in Queue, replacing Queue's use of property files. Updates to walkers used in existing QScripts to add @Input/@Output. RMD used in @Required/@Allows now has a new default equal to "any" type. New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions. Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.) Removed dependency on BroadCore by porting LSF job submitter to scala. Ivy now pulls down module dependencies from maven. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 00:42:48 +08:00
<ibiblio name="libraries" m2compatible="true" />
<ibiblio name="libraries_with_inconsistent_poms" checkconsistency="false" m2compatible="true" />
removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 08:42:37 +08:00
<ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4496 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 23:58:52 +08:00
<ibiblio name="java.net" m2compatible="false" root="http://download.java.net/maven/1/" pattern="[organisation]/jars/[artifact]-[revision].[ext]"/>
Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: - bsub command line is no longer fully printed out. - extraBsubArgs hack is now a callback function updateJobRun. Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q. Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits. Updated VE packages that live in oneoffs to compile to oneoffs. Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 12:36:06 +08:00
<ibiblio name="maven2-repository.dev.java.net" m2compatible="true" root="http://download.java.net/maven/2/" />
Move to ivy for dependency management. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@31 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 01:14:04 +08:00
</resolvers>
<modules>
<module organisation="edu.mit.broad" resolver="projects" />
<module organisation="net.sf" module="functionalj" resolver="projects" />
<module organisation="net.sf" module="samtools" resolver="projects" />
removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 08:42:37 +08:00
<module organisation="org.reflections" module="reflections" resolver="reflections-repo" />
adding a stripped down Tribble library for the start of integration git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2851 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 05:29:25 +08:00
<module organisation="org.broad" module="tribble" resolver="projects" />
Adding Jama for Ryan. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-27 22:30:36 +08:00
<module organisation="gov.nist" module="Jama" resolver="projects" />
Changed logging level to default at INFO instead of WARN. Changes to StingUtils command line for use in Queue, replacing Queue's use of property files. Updates to walkers used in existing QScripts to add @Input/@Output. RMD used in @Required/@Allows now has a new default equal to "any" type. New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions. Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.) Removed dependency on BroadCore by porting LSF job submitter to scala. Ivy now pulls down module dependencies from maven. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-10 00:42:48 +08:00
<!-- If colt fixes the version in the pom for 1.2.0 then this line can be removed. -->
<module organisation="colt" module="colt" resolver="libraries_with_inconsistent_poms" />
Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4496 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 23:58:52 +08:00
<module organisation="javax.mail" resolver="java.net" />
<module organisation="javax.activation" resolver="java.net" />
Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: - bsub command line is no longer fully printed out. - extraBsubArgs hack is now a callback function updateJobRun. Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q. Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits. Updated VE packages that live in oneoffs to compile to oneoffs. Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-10 12:36:06 +08:00
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
Killed sonatype repository; it's failed me too many times at this point. Temporarily disabled contracts in integrationtests until we can find the cause of the new error that's cropping up for Ryan. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5967 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-10 00:07:02 +08:00
<module organisation="com.google.code.caliper" resolver="projects" />
Switched GridEngine from looking from environment variable to using embedded jar.
2011-07-06 09:59:00 +08:00
<module organisation="net.sf.gridscheduler" resolver="projects" />
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests. The NullPointerException we were seeing when trying to run with contracts enabled was being caused by an outdated version of the asm library. To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant. Also did some minor unrelated cleanup in build.xml
2011-07-09 03:34:39 +08:00
<module organisation="com.google.code.cofoja" resolver="projects" />
Move to ivy for dependency management. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@31 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-12 01:14:04 +08:00
</modules>
</ivysettings>