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Re: Help needed to package manta which needs samtools >= 1.2 and libbam.a




----- Mail original -----
> De: "Andreas Tille" <andreas@an3as.eu>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Mardi 15 Novembre 2016 17:14:33
> Objet: Help needed to package manta which needs samtools >= 1.2 and libbam.a
> 
> Hi folks,
> 
> I have injected manta[1] into packaging Git.  Upstream contains several
> projects as tar.bz2 which are packaged for Debian and rebuilds these in
> the packaging process.  I tried to tweak the cmake input files to
> reference the Debian packaged alternatives.  I was stumbling about
> samtools (manta upstream contains version 1.2 - we just have 1.3 which
> might be a source of failure due to incompatibilities but lets ignore
> this for the moment).  The cmake build system needs a libbam.a which is
> only build by the legacy libbam-dev 0.1.19.  I wonder how we can get
> a libbam.a from recent samtools - or is there any other solution to
> build manta?

don't know how, but if it needs libbam.a, this means you are in static build, not using shared libraries, which is not the way Debian does.
So it seems you should tweak the make recipes to build with shared libraries instead of static compilation. this will solve your issue and use our .so files.


Olivier 

> 
> Here is the error message the current builds ends with:
> 
> ...
> make[3]: *** No rule to make target '/libhts.a', needed by
> 'src/c++/lib/applications/GenerateSVCandidates/test/manta_unit_test_GenerateSVCandidates'.
> Stop.
> make[3]: Leaving directory '/build/manta-1.0.2+dfsg/obj-x86_64-linux-gnu'
> CMakeFiles/Makefile2:1831: recipe for target
> 'src/c++/lib/applications/GenerateSVCandidates/test/CMakeFiles/manta_unit_test_GenerateSVCandidates.dir/all'
> failed
> ...
> 
> Kind regards
> 
>       Andreas.
> 
> [1] https://anonscm.debian.org/git/debian-med/manta.git
> 
> --
> http://fam-tille.de
> 
> 


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