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
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