Hello, 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: https://github.com/pbjd/pbutgcns <https://github.com/pbjd/pbutgcns> as well.
Sergey > On Dec 12, 2015, at 1:18 AM, Afif Elghraoui <[email protected]> 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 > <https://github.com/PacificBiosciences/FALCON/tree/master/src/py_scripts_v0.1> > > 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 > Afif > > 1. http://blends.debian.org/med/tasks/bio > 2. http://blends.debian.org/med/tasks/bio-dev > > -- > Afif Elghraoui | عفيف الغراوي > http://afif.ghraoui.name
