Hello everyone, I need your advice on a packaging issue I am meeting right now.I am in the course of packaging gatk-bwamem-jni [0], providing a native interface which allows one to use bwa (Debian packaged [1]) from Java code. Fine.
But the upstream of gatk-bwamem-jni relies on a version of bwa which is the tip of a -- now stale -- branch called "Apache2" in the Github repository of bwa. It cannot build against the Debian-packaged libbwa-dev as differences between the bwa branches "Apache2" and "master" are now too important.
What should I do? My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one + the sources at the tip of the Apache2 branch of bwa. It would build a libbwa.a lib which would not be installed in /usr/lib, but in a private directory of gatk-bwamem-jni. By doing so, I would not interfere with the currently Debian-packaged bwa and I would also be able to build, run and ship gatk-bwamem-jni... which would, still, be independent of the bwa that is shipped in Debian.
Does this seem sensible? Thanks a lot for your attention and help. Best regards, -- Pierre [0] https://github.com/broadinstitute/gatk-bwamem-jni [1] https://tracker.debian.org/pkg/bwa
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