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

[Nilesh Patra]

Package: igdiscover
Version: 0.11-4
Severity: serious
Usertags: ftbfs-bookworm

Dear Maintainer,

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, 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.

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.

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

-- System Information:
Debian Release: bookworm/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-2-amd64 (SMP w/8 CPU threads; PREEMPT)
Locale: LANG=en_IN, LC_CTYPE=en_IN (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages igdiscover depends on:
ii  python3              3.11.1-2
pn  python3-cutadapt     <none>
pn  python3-matplotlib   <none>
ii  python3-numpy        1:1.24.1-2+b1
pn  python3-pandas       <none>
pn  python3-ruamel.yaml  <none>
pn  python3-scipy        <none>
pn  python3-seaborn      <none>
pn  python3-sqt          <none>
pn  python3-xopen        <none>

igdiscover recommends no packages.

Versions of packages igdiscover suggests:
pn  igdiscover-doc  <none>
pn  snakemake       <none>