Fixed the Docker build to run using the jar

[jamesemery]

There is currently an issue with spark stderr output if running through the wrapper script, this is a workaround to that.

[droazen]

👍 Tested the new build command, and confirmed that the gatk script now uses the packaged jar instead of the unpackaged build. Merge when tests pass.

[codecov-io]

Codecov Report

Merging #4476 into master will increase coverage by 0.036%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #4476       +/-   ##
===============================================
+ Coverage     79.087%   79.124%   +0.036%     
- Complexity     16608     16647       +39     
===============================================
  Files           1049      1049               
  Lines          59672     59781      +109     
  Branches        9787      9815       +28     
===============================================
+ Hits           47193     47301      +108     
  Misses          8682      8682               
- Partials        3797      3798        +1

Impacted Files	Coverage Δ	Complexity Δ
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...park/sv/discovery/alignment/AlignmentInterval.java	89.655% <0%> (+0.383%)	74% <0%> (+1%)	⬆️
.../tools/walkers/mutect/SomaticGenotypingEngine.java	94.054% <0%> (+0.811%)	80% <0%> (+22%)	⬆️
...nder/utils/runtime/StreamingProcessController.java	70.37% <0%> (+0.823%)	50% <0%> (ø)	⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	80% <0%> (+1.29%)	39% <0%> (ø)	⬇️
...hellbender/tools/walkers/mutect/Mutect2Engine.java	91.045% <0%> (+2.156%)	52% <0%> (+7%)	⬆️
...ools/walkers/contamination/GetPileupSummaries.java	85.915% <0%> (+5.064%)	29% <0%> (+11%)	⬆️