Re: picard-tools: missing deps

[Olivier Sallou <olivier.sallou@irisa.fr>]

On 04/23/2018 05:00 PM, Olivier Sallou wrote:

I had a look to fix latest picard-tools and found there are missing deps:

   > Could not resolve com.intel.gkl:gkl:0.8.2.

     Required by:

         project :

      > No cached version of com.intel.gkl:gkl:0.8.2 available for offline mode.

      > No cached version of com.intel.gkl:gkl:0.8.2 available for offline mode.

   > Could not resolve org.broadinstitute:barclay:2.0.0.

     Required by:

         project :

      > No cached version of org.broadinstitute:barclay:2.0.0 available for offline mode.

      > No cached version of org.broadinstitute:barclay:2.0.0 available for offline mode.

those libs don't seem to be in debian.

after quick and dirty packaging of missing deps (locally), there are still other issues.
Jar packaging needs other deps (may try *simple* jar like was done before) but more annoying needs a specific jar patched from an other source:

org.broadinstitute:google-cloud-nio-GATK4-custom-patch:0.20.4-alpha-GCS-RETRY-FIX

can't find related sources, only generated jar (and rebuilding it seems we will again need additional deps... :-(   )
i have contacted picard team to get more info on this dependency [0]


[0] https://github.com/broadinstitute/picard/issues/1164

To avoid javadoc errors I found at first when building package, I locally updated build.gradle to remove all refs to javadocJDKFiles. This may not be valid when going to doc task, but wanted at least test to see if compilation etc was ok.... 

Olivier

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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