More robust determination of GATK version #1004
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DSP has updated the GATK website, breaking links to older versions. Tarballs for the older versions are preserved on GS with public links: https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk This commit updates the source url for the gatk 3.8 tarball to point to the new home on GS.
…is-fix-gatk-mindepth
…rsion set in TOOL_VERSION_TUPLE in gatk.py, when picking version-specific options
…oid Picked up _JAVA_OPTIONS message
tomkinsc
approved these changes
Feb 8, 2020
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When determining GATK version (e.g. for choosing version-specific switches), base it on the actual GATK jar, rather than on tools.gatk.TOOL_VERSION_TUPLE . Fix how GATK jar is extracted in refine_2x_and_plot task.
This PR includes the GATK URL updates from #1003 to make testing work.