Re: Kraken requires jellyfish version 1
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
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