Re: lofreq in Debian
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
On 6/1/16 14:03, Afif Elghraoui wrote:
Hi, Andreas,
I'm contacting you on behalf of the Debian Med team, a group within the
Debian project that aims to make Debian an ideal computing platform for
biology and medicine.
I took interest in packaging your software LoFreq, but was a bit
confused by the requirement for the samtools static library and internal
header files. It's my understanding that the samtools developers tried
to make all externally useful components available through htslib. Is
this something required for functionality of the software, or is it
needed only to provide the samtools functions faidx, index, and idxstats
as convenience clones within lofreq?
If the latter, we will probably patch those functions out for the Debian
package and have the lofreq package recommend the samtools package.
Please let me know your thoughts on this.
Many thanks for your work on lofreq and providing it under an agreeable
license.
regards
Afif
--
Andreas WILM, PhD
Research Associate
Computational and Systems Biology
Genome Institute of Singapore
http://www.gis.a-star.edu.sg
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