Hi Olivier, On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote: > > testing with your removals, you only need to add to build gradle file > the ref to htsjdk
I've now pushed the freshly stripped upstream version since we both agree that a competing htsjdk is not a good idea. > I pushed the update on patch (but your copyright patch is not yet there) > > With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar > removed from upstream source, it compiles fine for me. I confirm it compiles fine now. However: $ LC_ALL=C igv Error: Unable to initialize main class org.broad.igv.ui.Main Caused by: java.lang.NoClassDefFoundError: htsjdk/samtools/seekablestream/ISeekableStreamFactory Sorry to admit that we seem to need another iteration to get igv out. Thanks a lot for your effort Andreas. -- http://fam-tille.de