Re: lofreq in Debian
Thanks for your quick response. I am definitely linking dynamically to
htslib and have managed all the other dependencies. However, samtools
(as intended to be installed by its developers) is not supposed to
provide any library, as the externally useful functionality was supposed
to be made available through htslib.
I am simply wondering if you are using the samtools static library and
headers only for the convenience samtools functions you are making
available through lofreq. If this is the case, I am then asking if you
mind whether we remove those convenience functions from lofreq in the
Debian package.
Many thanks and regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
على الثلاثاء 5 كانون الثاني 2016 22:28، كتب Andreas WILM:
> Hi Afif,
>
> thanks for going through the effort of packaging LoFreq for Debian.
>
> Regarding your question: LoFreq is a mix of Python 2.7 scripts and C. It
> has a run-time dependency on Python 2.7, but none on samtools.
>
> During compile time however there is a dependency on the samtools and
> htslib (>=1.1) headers and their lib archives (libhts.a and libbam.a;
> see src/lofreq/Makefile.am). The full path to their corresponding
> directories needs to be defined with environment variables when running
> configure (see http://csb5.github.io/lofreq/installation/#source).
> zlib-devel is also required for installation from source (automatically
> found by configure). We wanted the package to be as stand alone as
> possible, hence the static linking against the htslib archives. For
> distributions it makes more sense to link it dynamically, but this will
> require some patching.
>
> Best regards,
> Andreas
>
>
> --
>
> Andreas WILM, PhD
> Research Associate
> Computational and Systems Biology
> Genome Institute of Singapore
> http://www.gis.a-star.edu.sg
>
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