Re: Competing arrow tools in pbgenomicconsensus and unanimity
On October 11, 2018 11:14:35 AM EDT, Andreas Tille wrote: >Hi Afif, > >On Thu, Oct 11, 2018 at 09:27:16AM -0400, Afif Elghraoui wrote: >> > >> >#!/bin/sh >> >variantCaller --algorithm=arrow $* >> > >> >while unanimity installs a compiled binary. @Afif (or whoever is >> >informed about this PB programs): Do you have a sensible suggestion >> >which arrow we should install? >> > >> >> At one point, I had read that unanimity was eventually going to >supersede pbgenomicconsensus altogether. Looking at the source tree >[3], it looks like genomicconsensus in unanimity is still marked >experimental, so I would stick with pbgenomicconsensus' implementation. >> >> As for the name, "arrow" succeeds "quiver", so there's a little theme >going on. And quiver had some meaning as a Quality Value-aware variant >caller. > >My conclusion from your answer is that it makes sense to ship arrow >from >unanimity while removing the little wrapper from pbgenomicconsensus. >This can be explained in d/NEWS.Debian. > >Do you agree with this conclusion? > No, that's the opposite of what I said. The unanimity implementation looks like it's still experimental. Afif
Re: Competing arrow tools in pbgenomicconsensus and unanimity
Hi Afif, On Thu, Oct 11, 2018 at 09:27:16AM -0400, Afif Elghraoui wrote: > > > >#!/bin/sh > >variantCaller --algorithm=arrow $* > > > >while unanimity installs a compiled binary. @Afif (or whoever is > >informed about this PB programs): Do you have a sensible suggestion > >which arrow we should install? > > > > At one point, I had read that unanimity was eventually going to supersede > pbgenomicconsensus altogether. Looking at the source tree [3], it looks like > genomicconsensus in unanimity is still marked experimental, so I would stick > with pbgenomicconsensus' implementation. > > As for the name, "arrow" succeeds "quiver", so there's a little theme going > on. And quiver had some meaning as a Quality Value-aware variant caller. My conclusion from your answer is that it makes sense to ship arrow from unanimity while removing the little wrapper from pbgenomicconsensus. This can be explained in d/NEWS.Debian. Do you agree with this conclusion? Kind regards Andreas. -- http://fam-tille.de
Re: Competing arrow tools in pbgenomicconsensus and unanimity
Hello, On October 11, 2018 8:06:26 AM EDT, Andreas Tille wrote: >Hi, > >package unanimity[1] now builds and creates the binary package >python-consensuscore2 which in turn is needed to build the latest >version of pbgenomicconsensus[2]. I realised that both packages are >installing a tool /usr/bin/arrow (shame on upstream for this generic >name ;-)). In pbgenomicconsensus its a simple script > >#!/bin/sh >variantCaller --algorithm=arrow $* > >while unanimity installs a compiled binary. @Afif (or whoever is >informed about this PB programs): Do you have a sensible suggestion >which arrow we should install? > At one point, I had read that unanimity was eventually going to supersede pbgenomicconsensus altogether. Looking at the source tree [3], it looks like genomicconsensus in unanimity is still marked experimental, so I would stick with pbgenomicconsensus' implementation. As for the name, "arrow" succeeds "quiver", so there's a little theme going on. And quiver had some meaning as a Quality Value-aware variant caller. regards Afif > > >[1] https://salsa.debian.org/med-team/unanimity >[2] https://salsa.debian.org/med-team/pbgenomicconsensus [3] https://github.com/PacificBiosciences/unanimity/tree/develop/src
Competing arrow tools in pbgenomicconsensus and unanimity
Hi, package unanimity[1] now builds and creates the binary package python-consensuscore2 which in turn is needed to build the latest version of pbgenomicconsensus[2]. I realised that both packages are installing a tool /usr/bin/arrow (shame on upstream for this generic name ;-)). In pbgenomicconsensus its a simple script #!/bin/sh variantCaller --algorithm=arrow $* while unanimity installs a compiled binary. @Afif (or whoever is informed about this PB programs): Do you have a sensible suggestion which arrow we should install? Kind regards Andreas. [1] https://salsa.debian.org/med-team/unanimity [2] https://salsa.debian.org/med-team/pbgenomicconsensus -- http://fam-tille.de
