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Re: CI for kraken

Hello Nadiya,

On Thu, Jul 20, 2017 at 04:38:08PM -0700, Nadiya Sitdykova wrote:
> I can see a git repository jellyfish1, but I'm not sure how to tell kraken
> to use this particular package.

Well, for sure you add this to the dependencies.

> I tried to write jellyfish1 in debian/control Depends and it didn't work.
> Also I tried jellyfish (= 1.1.5-1) and it still gives the same error
> message.
> And when I try just jellyfish it doesn't work again with message
> Found jellyfish v2.2.6
> Kraken requires jellyfish version 1
> Sorry, I must be missing something important.

I have no time to track this down before Monday, but here are some

  1. We need to make yellyfish and jellyfish1 co-installable -
     currently the executables have the same name - so jellyfish1
     should have /usr/bin/jellyfish1
  2. Since kraken will not seek for /usr/bin/jellyfish1 we either
     need to put the jellyfish1 executable in /usr/lib and provide
     the binary above as link.  Than we could use a shell wrapper
     around kraken and set the PATH accordingly to make sure kraken
     will find the right executable.
     Alternatively we can simply patch kraken to use jellyfish1.
     This might be easier to debug to make really sure that kraken
     is using the correct version and it should definitely prevent
     that it will find the 2.2.6 version.

So far for my ideas.  If these are not helpful I need to check at
beginning of next week.

Kind regards



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