[Debian-med-packaging] Bug#995406: bbmap: package does not ship resource files

[Andreas Tille]

Control: tags -1 pending

Hi Robert,

thanks a lot for the

Am Thu, Sep 30, 2021 at 01:22:23PM -0400 schrieb Robert:
> The bbmap package does not ship the needed resource files which causes some of
> the included tools not to work, e.g. bbduk when trying to process some fastq
> data, crashes with output like [1].

Thanks a lot for the report.  Its extremely helpful since several of our
maintainers are not using this software and we really need to rely on
user input.
 
> I don't have a census which other bbtools require resource files to be usable,
> but bbduk is not usable at all in the current state.
> 
> My suggested fix (see patch [2]) puts the resource files to the root of
> the built jar file.  This is were dna.Data.findPath() will indeed find
> these files, which can be seen when looking at the verbose output [3]
> for findPath() (by setting vb=true in current/dna.Data.java near line
> 1204).  By contrast, the current packaging tries (but also fails) to put
> the files under resources/.  I don't see a way to trick jh_build with
> the JH_JAR_EXTRA mechanism to do what is needed (without changes to
> jh_build).  The patch applies agaiinst the bbmap source package's
> current git master branch and the package builds and run for me on
> bullseye.

I've pushed your patch to Git and can upload soon, but I wonder wether
we could your use case use as autopkgtest.
 
> $ pwd
> /tmp/bbduk_test
> $ ls
> fwd.fastq  rev.fastq

Could you provide these data as examples - or do you have some similar
ones we could use.

> $ bbduk.sh in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe tbo threads=48 out=out.fastq
> java -ea -Xmx76702m -Xms76702m -cp /usr/share/java/bbmap.jar jgi.BBDuk in1=fwd.fastq in2=rev.fastq ktrim=r k=21 mink=8 hdist=2 ftm=5 tpe tbo threads=48 out=out.fastq
> Executing jgi.BBDuk [in1=fwd.fastq, in2=rev.fastq, ktrim=r, k=21, mink=8, hdist=2, ftm=5, tpe, tbo, threads=48, out=out.fastq]
> Version 38.90
> 
> Set threads to 48
> maskMiddle was disabled because useShortKmers=true
> Warning!  Cannot find primes.txt.gz /tmp/bbduk_test/file:/usr/share/java/bbmap.jar!/primes.txt.gz
> 	at jgi.BBDuk.main(BBDuk.java:78)

If we could turn this into a test I could upload including test.

Kind regards

      Andreas. 

-- 
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