On Fri, Nov 20, 2015 at 3:05 AM, Andreas Tille <[email protected]> wrote:
> Hi again, > > to summarise my last mail it boils down to two questions: > > To kraken author: > Would kraken rund with jellyfish 1.5.5? > I think it should. > > To jellyfish author: > In what jellyfish version was the output format changed? > > The format changed with version 2.0. Truth be told, the formats are very close to one another. Only the header has changed. It used to be a fixed number of fields in binary, it changed to a JSON formatted header, containing much more information. But the rest of the file, past the header, should be identical. Changing one file format to the other should be easy. Guillaume. > 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 <[email protected]> > 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 >
