75c1987a18
fixed the build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3143 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-09 13:03:31 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +00:00
a6e8687d71
implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 04:20:19 +00:00
9e107513d0
In the new sharding system, if no read group is present, hallucinate one. Added
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for test compatibility, but not sure whether we still need this feature. TODO: Poll the group about this feature.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2949 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 23:01:34 +00:00
adea38fd5e
Sharding system fixes for corner cases generally related to lack of coverage
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in the BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2928 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 18:59:21 +00:00
c1f154c31f
Fully qualify the target for the output file so that external build processes (aka firehose)
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won't aren't impacted when building the GATK from outside the base directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2696 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 23:06:30 +00:00
169032aa78
Add new 'release' task to push releases into a shared directory and the website.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2695 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 22:50:20 +00:00
022601b1a5
Warnings for walkers w/o Javadoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:34:50 +00:00
8dafd26100
Print out the current version number in the application header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2633 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:58:36 +00:00
1488578617
Working with Aaron to get svnversion running within the build system. This change will break the build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2628 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 16:55:42 +00:00
d2961a3a17
Typo in previous commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2610 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:41:42 +00:00
45de006ca3
Disable extraction of svn info completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2609 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:30:25 +00:00
8ce79e002c
Fix for failed build. Seems to be an issue with Bamboo environment. I'll
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discuss w/ Aaron next week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2608 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 01:06:26 +00:00
ac4756db20
Add the svn version on the fly to the version number properties.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2607 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-16 00:28:01 +00:00
420cef4094
Added version numbers to the help doclet extractor. Since the help system is behaving
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more like a resource bundle at this point, changed it over to use the Java ResourceBundle
support classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2606 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 23:31:29 +00:00
4617052b3c
For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2457 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-28 23:42:46 +00:00
d75d3a361a
Clean up some of the walker help output based on additional experience and
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:33:11 +00:00
10be5a5de9
Move some files around to reflect our growing help infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:23:12 +00:00
16ef500139
Tweak the build.sysclasspath option to force the system classpath to always be appended to additional jars added to the classpath by us. These seemed to be set differently depending on the platform or distribution before.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2279 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:19:29 +00:00
4c147329a9
Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 20:08:41 +00:00
d27d56ea0c
adding the option to not halt after a test failure; it will still report failure at the end. This makes sense for Bamboo so we know all the tests that fail, not just the first. It is also useful for checking what tests are affected by a change.
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You can tell ant not to halt with: 'ant -Dhalt=no' (yes is the default)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2240 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:19:39 +00:00
2460f2a789
minor update to build.xml for CG utilities. Hopefully bamboo will be back online
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2237 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 00:06:02 +00:00
0b6b92bf5b
Fix (hopefully) the rest of the problems with the build.xml svn merge.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2236 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:53:31 +00:00
f41965a73e
Fixed incompatiblity in variable name between my script and the new elements merged into my script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2235 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:40:50 +00:00
357abc9e89
Update build.xml to make it oneoffprojects-aware, and do some misc formatting cleanup and moves.
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Here goes nothing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2234 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:27:45 +00:00
c524b8e84b
add VCFTool.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2221 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:04:38 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
b7097a8db9
Build aligner as separate jar file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2044 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:29:29 +00:00
8eff1cc436
Extract and include only the Tim Fennell-approved parts of picard private.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:42:33 +00:00
21b1ece45d
removed some extra debugging commands from the build.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1972 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 06:28:12 +00:00
c313abf0be
Restore a jar packaging change that got clobbered.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1962 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:15:45 +00:00
de6ae51f7e
Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 06:02:41 +00:00
b95165e39c
Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 00:33:18 +00:00
5a64a80ab5
changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:31:33 +00:00
d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
0df6a9da5c
-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:01:40 +00:00
515fc7c476
overaggressively removed the STD outputs, back in for tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1514 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:07:45 +00:00
7d0a13d711
added options for building with xml output to files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1513 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:00:27 +00:00
6c604af86c
Nicer building of scala programs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1476 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 16:41:56 +00:00
ab9458d06d
support for scala walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1468 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:15:01 +00:00
f3e63f00bc
Exclude secondary base caller code from playground jar. Still TODO: figure
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out how do deal with the playground jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1344 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:02:46 +00:00
f7168bd7cf
added the abilty to build the jar's to a different location, like the following:
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ant -Ddist=altDist
or
ant -Ddist=/where/you/want/jars
Also changed the test build to depend on playground build instead of core, right now tests fail if you only build the core.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1299 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 04:06:58 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
e2ccea4883
Cleanup. Move output of packaging to dist directory. Don't always create resources directory. Make jar take on the package name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1023 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:47:23 +00:00
29df74ae23
Plumbed packaging support into build.xml and added package for GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:41:16 +00:00
94b0e46d12
checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:46:16 +00:00
3a340ca887
adding the SomaticCoverage.jar to the list of generated jars, at least for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@977 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:05:54 +00:00
57e5f22987
We now only build the files that have changed. It should speed up compile time as our source tree grows.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@726 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:48:01 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
aaron
hanna
depristo
jmaguire
rpoplin
kiran