[Debian-med-packaging] Help to detect java classes in drop-seq (covid-19 relevant) needed

[Andreas Tille]

Hi,

I've started packaging of drop-seq[1] and replaced those JARs that are
replacable by Debian packaged versions.  I also have set CLASS_PATH in
d/rules, but it seems to be ignored.  I have dealt with similar cases by
patching it into build.xml but here I have not found the relevant place
to do so.  I'm aware that I did not yet added all needed classes to
CLASS_PATH, but currently I get


   dh_auto_build
        ant -Duser.name debian
Buildfile: /build/drop-seq-2.3.0+dfsg/build.xml
  [taskdef] Could not load definitions from resource testngtasks. It could not be found.

compile-src:
    [mkdir] Created dir: /build/drop-seq-2.3.0+dfsg/classes
    [javac] Compiling 201 source files to /build/drop-seq-2.3.0+dfsg/classes
    [javac] /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:28: error: package htsjdk.samtools does not exist
    [javac] import htsjdk.samtools.SAMException;
    [javac]                       ^
    [javac] /build/drop-seq-2.3.0+dfsg/src/java/org/broadinstitute/dropseqrna/TranscriptomeException.java:34: error: cannot find symbol
    [javac] public class TranscriptomeException extends SAMException
    [javac]                                             ^
    [javac]   symbol: class SAMException
...


but /usr/share/java/htsjdk.jar which is in CLASS_PATH contains this class.

Any hint how to take this hurdle would be welcome.

Kind regards

       Andreas.


[1] https://salsa.debian.org/med-team/drop-seq

-- 
http://fam-tille.de