Add jitpack support for SNAPSHOTS

[magicDGS]

Closes #4819

[magicDGS]

@lbergelson - maybe you can have a look, as you commented in the original issue. As the commit isn't in the repo yet, I cannot test if it is working here. But here are the logs for the commit in the repo where I did the change: https://jitpack.io/com/github/bioinformagik/gatk/6270fa279/build.log

[codecov-io]

Codecov Report

Merging #5056 into master will increase coverage by 0.02%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##             master    #5056      +/-   ##
============================================
+ Coverage     86.35%   86.37%   +0.02%     
- Complexity    28824    29156     +332     
============================================
  Files          1791     1814      +23     
  Lines        133601   135364    +1763     
  Branches      14920    15042     +122     
============================================
+ Hits         115364   116914    +1550     
- Misses        12834    12996     +162     
- Partials       5403     5454      +51

Impacted Files	Coverage Δ	Complexity Δ
...ender/tools/spark/sv/utils/GATKSVVCFConstants.java	0% <0%> (-75%)	0% <0%> (-1%)
...s/spark/ParallelCopyGCSDirectoryIntoHDFSSpark.java	0% <0%> (-74.257%)	0% <0%> (-17%)
...nder/tools/spark/pipelines/PrintVariantsSpark.java	0% <0%> (-66.667%)	0% <0%> (-2%)
...oadinstitute/hellbender/utils/test/XorWrapper.java	13.043% <0%> (-65.217%)	2% <0%> (-7%)
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	54.194% <0%> (-25.806%)	30% <0%> (-10%)
...nder/tools/spark/BaseRecalibratorSparkSharded.java	0% <0%> (-22.807%)	0% <0%> (-2%)
...bender/tools/walkers/annotator/ReferenceBases.java	83.333% <0%> (-16.667%)	6% <0%> (+1%)
...titute/hellbender/utils/test/MiniClusterUtils.java	78.947% <0%> (-10.526%)	6% <0%> (-1%)
...org/broadinstitute/hellbender/utils/BaseUtils.java	86.726% <0%> (-3.54%)	46% <0%> (-2%)
... and 106 more

[lbergelson]

@magicDGS I have a few suggestions. Have you tested that this works or is that impossible until it's merged?

[lbergelson]

I'd use a more recent version, maybe probably 2.5.1 since it's the most recent.

[magicDGS]

Done

[lbergelson]

You should use git lfs pull --include src/main/resources/large which only downloads the ~50mb of files required to build gatk rather than the 3+ gb of test resources required to test it as well.

[magicDGS]

Done

[lbergelson]

If it's possible to add comments to this yaml, could you add one explaining what it is for people who aren't familliar with jitpack.

[magicDGS]

I will first push the next changes to test the build (can also be tested from the fork, as this branch is not part of this repo) and then try to add the comments (jitpack have very bad documentation for the yml, I extracted the info from https://jitpack.io/docs/BUILDING/#custom-commands)

[magicDGS]

Done (only adding a purpose comment) - let me know if you would like more info

[lbergelson]

Could you add a comment to this file explaining what it is for people who don't know what jitpack is.

[magicDGS]

Done

[magicDGS]

@lbergelson - the last commit works. Check the logs and artifacts in this folder: https://jitpack.io/com/github/bioinformagik/gatk/336d389ecc605f4138226dddda41981f78278e09

[magicDGS]

Back to you @lbergelson - also, do you think that this will still work after #5112?

[lbergelson]

@magicDGS It looks like jitpack runs ./gradlew install ( https://jitpack.io/docs/BUILDING/#gradle-projects ) which will create both the normal and testutils jars after that's split out. So it should be fine. You'll obviously have to change how you import the jars to include the test utils jar but there's no getting around that.

[lbergelson]

@magicDGS Thanks for doing this.