In what version of Jellyfish has the database output format changed (Was: Kraken requires jellyfish version 1)

[Andreas Tille <andreas@an3as.eu>]

Hi Guillaume,

as you might know the Debian Med team is packaging Jellyfish for a
couple of releases.  After discussion with Derrick Wood the author of
Kraken[1] I learned that Jellyfish 2 has changed its output format.  To
enable Kraken working properly I decided to also package the latest
Jellyfish version 1 with the old output format.

So I checked out the latest jellyfish 1 version which is 1.5.5.  When
doing so I noticed that it contains a file

   jellyfish-2.0.pc.in

which leads to the installation of the following dynamic library

   /usr/lib/libjellyfish-2.0.so.2.0.0

Since I was not able to find any documentation about a change in the
output format (I admit I was seeking only inside the source code README
files not the web or the code itself) I'm now wondering in what exact
version the format change happened.  The bumped library version to 2.0
inside the Jellyfish 1.5.5 source package looks a bit suspicious to
me and before I do something wrong I'd like to ask.

Kind regards

        Andreas.

[1] http://ccb.jhu.edu/software/kraken/

On Mon, Nov 16, 2015 at 09:08:05PM -0500, Derrick Wood wrote:
> 
> On Mon, Nov 16, 2015 at 10:59 AM, Andreas Tille <andreas@an3as.eu> wrote:
> 
> > Hi Derrick,
> >
> > On Mon, Nov 16, 2015 at 10:20:07AM -0500, Derrick Wood wrote:
> > > I'm pleased to hear that Kraken's got a Debian package.
> >
> > You are welcome. :-)
> >
> > > As for Jellyfish
> > > v1, unfortunately, JF v2 changed the output file format,
> >
> > That's an unfortunate choice. :-(
> >
> > > and so Kraken will
> > > need a bit of work to handle the new files properly. I'm working on
> > Kraken
> > > 2 at the moment, and that does not use Jellyfish at all.
> >
> > Could you provide any time scale (like will take some weeks or several
> > monthes) until there might be some test candidates for Kraken 2?
> >
> > > I may be able to
> > > modify a few things in the Kraken 1 code to handle JF2 files, but I
> > haven't
> > > done enough work with JF2 to ensure that it will work properly in all
> > > situations that Kraken needs it to.
> >
> > I could imagine that its not fun to support this while working on a new
> > version without any Jellyfish.
> >
> > > I have actually just thought of
> > > distributing JF1 (either compiled or source, I'm undecided) with Kraken
> > so
> > > that Kraken's build will use its own Jellyfish program regardless of what
> > > is installed system-wide.
> >
> > Hmmm, that would not help much from a Debian perspective.  We do not
> > really like code copies.  My alternative suggestion would be the
> > following:
> >
> >    1. Create a jellyfish1 package providing
> >        /usr/lib/jellyfish1/jellyfish
> >       (and provide the binary via
> >        ln -s /usr/lib/jellyfish1/jellyfish /usr/bin/jellyfish1
> >        but that should be irrelevant for kraken)
> >
> >    2. Use wrapper scripts for kraken like /usr/bin/kraken-build:
> >
> >       #!/bin/sh
> >       export PATH=/usr/lib/jellyfish1/jellyfish:$PATH
> >       /usr/lib/kraken/kraken-build $@
> >
> > This way Kraken will find jellyfish version 1 first in the PATH and
> > should work as expected.
> >
> > If you consider that it takes some time until you might finish Kraken 2
> > I could implement this for the time beeing.
> >
> > Kind regards
> >
> >         Andreas.
> >
> > --
> > http://fam-tille.de
> >

-- 
http://fam-tille.de