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Re: Packaging the Celera Assembler for Debian - PBcR dependency on Falcon


The falcon_sense binary is a PyInstaller binary built from the falcon_sense.py script to ease distribution for users so they don’t have to build/checkout all of Falcon’s codebase. If you build Falcon version 0.1.3, it should be compatible with PBcR. You would need to strip the .py of the file end and make sure it is executable so the PBcR pipeline will be able to run it as falcon_sense (without the .py and without specifying python). As long as it is in your path, it will be picked up by PBcR. As for pbutgcns, it is not required but does speed up the overall pipeline, you should also be able to build it from source:
as well.


On Dec 12, 2015, at 1:18 AM, Afif Elghraoui <afif@ghraoui.name> wrote:

Hi, Dr. Koren,
I'm contacting you on behalf of the Debian Med team, a group within the
Debian project that packages biological and medical software. You might
be interested to see lists of the biological software we have made
available in Debian [1-2].

I've been working on packaging the Pacific Biosciences' SMRTAnalysis
suite and therefore came to the Celera assembler. Following Debian
policy, we must build all packaged programs from source, and we have so
far most of the dependencies of wgs-assembler in Debian.

The only remaining dependencies I see missing are Falcon (and pbutgcns,
but that does not appear to be essential). For the PBcR module, I see
that the falcon_sense binary that you redistribute is not provided by
the Falcon package anymore-- it exists in deprecated form as a python
script--not a compiled executable---at

What do you recommend for this situation with Falcon? We just need to be
able to build all the components from source.

Many thanks and regards

1. http://blends.debian.org/med/tasks/bio
2. http://blends.debian.org/med/tasks/bio-dev

Afif Elghraoui | عفيف الغراوي

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