[Debian-med-packaging] Bug#1032975: igdiscover -- Broken, unusable package due to incomplete code in the binary package

[Andreas Tille]

Hi Nilesh,

Am Wed, Mar 15, 2023 at 07:45:52AM +0530 schrieb Nilesh Patra:
> igdiscover vendors just a /usr/bin/igdiscover with is supposed to be
> nothing more than just a wrapper. The actual code is missing from the
> binary package (i.e. the python files) effectively making igdiscover
> useless.
> 
> Even after fixing that,

Thanks a lot for your work in the first place.

> igdiscover is still broken because of a broken
> Snakefile and it is not able to run the pipeline/workflow which is the
> main functionality here (it is a workflow tool).
> 
> Steps to check can be found here[1]. Remember to change merge tool to
> 'flash' (and apt-get install flash) before running `igdiscover run`.
> It chokes at not being able to find "igblastn" -- it might be originatin
> from ncbi-igblast.

As far as I understood igdiscover needs igblast (source package is
ncbi-igblast) and I was working together with Aaron to get this packaged.
The version of igdiscover in Git had probably fixed the binary code so
this dependency became more obvious.  The reason why I did not uploaded
it was the lack of igblast at the time when I was working in igdiscover.
Unfortunately I missed comming back once igblast was finally accepted
and thus igdiscover remained unfixed / not updated.

> I've fixed the first part (py files installation) and pushed changes to
> salsa in a different branch here[2]. I do not have any more time to look
> into it.

Thanks for all your work on this.

@Steffen, could you please raise your opinion what to do with this
package.  Is it worth to spent time in the old version of igdiscover or
should we simply release bookworm without it, fix the latest version and
upload it to backports once bookworm is released?  Possibly the latest
version is also just a bugfix release and you (Steffen) talk to the
release team giving good reasons why we need that version and why it is
important to have this package in Debian.

However, even the latest version in Salsa needs fixing.  I re-activated
the build-time tests to show the log in CI but somehow CI is not working
currently - feel free to clone and build yourself to see what happens.

IMHO igdiscover is not ready for release and we should probably remove
it from testing.

Kind regards
    Andreas.

> [1]: https://docs.igdiscover.se/en/stable/testing.html
> [2]: https://salsa.debian.org/med-team/igdiscover/-/tree/bookworm-release

-- 
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