046cecb067
Switched our code over to the new command line style (gnu style args), added the initial logger code, and added apache commons CLI to the IVY script.
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There will be a slow conversion of all the System.out and System.err in other files to the logger style output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@145 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-22 21:06:22 +00:00
1fcf4c0cbf
Update picard to work with new samtools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:51:26 +00:00
7bc45b68aa
Added dependences on two libraries: the Colt package, which is a collection of high performance computing libraries from CERN; and Log4j, which will be our new logging platform.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@100 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 16:16:31 +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