GATK 1.4 tools -- updated all after MTS is updated to run these in a Py2 env

[jennaj]

galaxyproject/tools-devteam#546

[jennaj]

Workaround for End-Users

It is strongly recommended to use updated variant analysis methods

See the GTN Tutorials: https://training.galaxyproject.org/training-material/topics/variant-analysis/

Note: All GATK tools wrapped for Galaxy should be avoided or expect problems.: GATK 1.4 tools have been deprecated for several years. They remain on the usegalaxy.org server for backward compatibility reasons. There is some work to create wrappers for GATK4 tools but that is still a work in progress. Any GATK 2 or 3 release tools, that may be wrapped in the ToolShed (usegalaxy.org/toolshed) or found at other public Galaxy servers, are all considered deprecated/problematic to some degree.

[natefoo]

This should now be fixed. There's no tool update, the fix was some clever job running hackery by @mvdbeek in #288.

[jennaj]

Note for end-users:

Again, all GATK 1.4 tools are deprecated and should be avoided. Several have known issues unrelated to this particular correction. Your job may not even fail, but instead, produce putatively "successful" results are scientifically incorrect.

It is strongly recommended to use updated variant analysis methods

See the GTN Tutorials: https://training.galaxyproject.org/training-material/topics/variant-analysis/

The ONLY valid and current GATK tool at this time is:

GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes (Galaxy Version 4.1.4.0+galaxy2)