Hi again,
to summarise my last mail it boils down to two questions:
To kraken author:
Would kraken rund with jellyfish 1.5.5?
To jellyfish author:
In what jellyfish version was the output format changed?
Kind regards
Andreas.
--
On Tue, Nov 17, 2015 at 09:52:24AM +0100, Andreas Tille wrote:
> 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
http://fam-tille.de