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
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