[Debian-med-packaging] Bug#1071435: ugene: Plugins not found by Ugene

[Kalan Walmsley]

Package: ugene
Version: 50.0+dfsg-1
Severity: important
Tags: l10n
X-Debbugs-Cc: info at kalankaboom.net

Dear Maintainer,

   * What led up to the situation?
     I installed package `ugene`.
   * What exactly did you do (or not do) that was effective (or
     ineffective)?
     Running `ugeneui` and checking the installed plugins menu.
   * What was the outcome of this action?
     No plugins were listed in the plugin manager.
   * What outcome did you expect instead?
     That the installed plugins would be listed.

After some research, I found that Ugene requires that its `plugins`
directory be in the same directory as its executables (`ugene`, `ugeneui`,
etc.). I can see that the plugins are installed in `/lib/ugene/plugins`, so the
issue is just that `ugene` cannot find them. This issue seems similar to
[this one on GitHub](https://github.com/ugeneunipro/ugene/issues/293).

Could a symlink maybe be useful in this case?

Thank you very much for your help!

-- System Information:
Debian Release: trixie/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.7.12-amd64 (SMP w/20 CPU threads; PREEMPT)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages ugene depends on:
ii  libc6                   2.38-11
ii  libgcc-s1               14-20240330-1
ii  libgl1                  1.7.0-1+b1
ii  libglu1-mesa [libglu1]  9.0.2-1.1+b1
ii  libqt5core5t64          5.15.10+dfsg-7.2+b1
ii  libqt5gui5t64           5.15.10+dfsg-7.2+b1
ii  libqt5network5t64       5.15.10+dfsg-7.2+b1
ii  libqt5printsupport5t64  5.15.10+dfsg-7.2+b1
ii  libqt5script5           5.15.10+dfsg-3+b1
ii  libqt5scripttools5      5.15.10+dfsg-3+b1
ii  libqt5svg5              5.15.10-2+b2
ii  libqt5test5t64          5.15.10+dfsg-7.2+b1
ii  libqt5widgets5t64       5.15.10+dfsg-7.2+b1
ii  libqt5xml5t64           5.15.10+dfsg-7.2+b1
ii  libsqlite3-0            3.45.3-1
ii  libstdc++6              14-20240330-1
ii  libx11-6                2:1.8.7-1+b1
ii  libxtst6                2:1.2.3-1.1+b1
ii  ugene-data              50.0+dfsg-1
ii  zlib1g                  1:1.3.dfsg-3.1

Versions of packages ugene recommends:
ii  bedtools                2.31.1+dfsg-2
ii  bowtie                  1.3.1-3
ii  bowtie2                 2.5.3-1
ii  bwa                     0.7.17-7+b3
pn  clark                   <none>
ii  clustalo                1.2.4-8
ii  clustalw                2.1+lgpl-7
ii  cutadapt                4.7-2
ii  default-jre-headless    2:1.17-75
ii  fastqc                  0.12.1+dfsg-3
ii  hisat2                  2.2.1-4+b3
ii  hmmer                   3.4+dfsg-2
ii  hmmer2                  2.3.2+dfsg-12
ii  kalign                  1:3.4.0-1
ii  kraken                  1.1.1-4
ii  macs                    3.0.1-2
ii  mafft                   7.505-1
ii  metaphlan [metaphlan2]  4.0.4-1
ii  mrbayes                 3.2.7a-7+b1
ii  muscle                  1:5.1.0-1
ii  ncbi-blast+             2.12.0+ds-4+b1
ii  phyml                   3:3.3.20220408-3+b1
ii  primer3                 2.6.1-4
ii  r-base                  4.4.0-2
ii  samtools                1.19.2-1+b1
ii  spades                  3.15.5+dfsg-7
ii  t-coffee                13.45.0.4846264+really13.41.0.28bdc39+dfsg-1
ii  trimmomatic             0.39+dfsg-2
ii  vcftools                0.1.16-3+b1
pn  wevote                  <none>

Versions of packages ugene suggests:
pn  cufflinks  <none>

-- no debconf information