About gatk -- git-lfs and dependencies to be packaged

[Pierre Gruet <pgt@debian.org>]

Hi everyone,

Recently there has been quite a lot of movement around the packaging of 
gatk:

- I listed the dependencies to be packaged in our common spreadsheet, in 
the Java sheet, on lines 61 to 78. I think some of them should reveal 
optional, but I also see at some point we will be blocked by the need 
for Scala 2.12, whereas we only have 2.11 in Debian. This is a blocker 
we have already met on other packages;

- Nilesh and Yadd could find a new formulation for debian/watch which 
seems to enable us to use the git-lfs features to get the whole source 
tarball:

cat debian/watch

version=4
     opts="mode=git, gitmode=full, pgpmode=none" \
     https://github.com/broadinstitute/gatk.git \
     refs/tags/v?([\d\.]+) debian

Yet I gave it a try and the whole source is approx. 9.5 GB large and the 
(not repacked) orig tarball is 3.7 GB large. Thus we should do some work 
to strip a lot of big files, which I think would amount to deactivating 
some tests.

- Steffen and I looked at the dependencies list I discussed above and we 
wondered if getting gatk packaged now was worth the effort...
In any case, the Scala issue should be fixed, maybe we should have a 
discussion with the Scala team to see how we could stop being stuck with 
our old Debian-packaged Scala.


Best,

--
Pierre