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
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +00:00
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +00:00
89344ccc0f
Not sure why junit is so excited about running inner classes with no @Tests.
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Omit inner classes from the fileset of tests to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@595 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 21:56:34 +00:00
b6a7ebd3c4
You can now test a single JUnit test from the command line, by specifying the test with the command line parameter -Dsingle=myTestName.
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example:
ant test -Dsingle=TraverseReadsTest
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@559 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 13:30:47 +00:00
4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
32e000bbfe
Added MatchSQTagToStrand jar target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@377 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:50:36 +00:00
49fd951d8c
Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@364 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-11 21:10:42 +00:00
a2a38a4bbb
Removed RepairBadlyCombinedSamFile jar target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@359 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:21:19 +00:00
8efedacabf
Bump sam jdk to svn rev 207.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@340 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 22:16:46 +00:00
decf45664a
Removed now-useless FourBaseCaller jar target (FourBaseRecaller replaces it).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@277 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:13:51 +00:00
cb6a3b7e55
Bug fix: build couldn't be forced to core. Now it can be.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@221 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 01:36:25 +00:00
c4f0b4cab7
Oops. Javadoc output gets a lot cleaner when I remember to add the classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@220 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:29:20 +00:00
74cae62ac2
Cleaned up generation of javadoc code. Still need to fix javadoc generation to take external dependencies into account.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@219 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:03:08 +00:00
fade36a8f2
Add targets to force build to core and force build to playground.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@216 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 22:32:44 +00:00
1d95f06ad5
Fix path issue generating javadocs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@202 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 18:51:56 +00:00
9e2a373184
Prototype, buggy implementation of walker command-line arguments. Doesn't
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(yet) deal elegantly with even simple cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 00:12:00 +00:00
c047b53d6b
added some cleanup of code, and new junit targets to the build file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@177 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 21:16:12 +00:00
a55d630ef9
Added FourBaseRecaller to list of jar targets (this is just until I figure out the appropriate way to combine FourBaseCaller and FourBaseRecaller).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@172 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:10:48 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
411e5cf647
Added FourBaseCaller as a jar build target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@128 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-21 17:59:13 +00:00
ffb6f8f5da
Move the basic gatk framework into the core subtree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@95 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:39:00 +00:00
1096bbd4d9
Moved build.xml, ivy.xml and settings to root of Sting repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@88 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 19:13:19 +00:00
aaron
hanna
kiran