MiModD unresolved dependencies

,
1

I installed the suite_mimodd from Galaxy. However, when I tried to install the dependencies, it continues to say “unresolved.” I tried selecting MiModD, samtools, and bcftools and installing the dependencies using Conda as it states here: Galaxy Toolshed Installation – MiModD 0.1.9 documentation, but it keeps failing. I have tried “Using resolvers of type” with “Conda” and also with “any,” but I always get dependencies “unresolved.” How can I fix this issue?

Thank you

2

ok, a bit more information is needed to debug this:

  1. How did you obtain and install Galaxy
  2. Have you successfully installed any other tools from the toolshed
  3. Which OS are you runnng this on
  4. Have you tried to install the different mimodd repos individually instead of via the suite

Together we should be able to figure things out :slight_smile:

Cheers,

Wolfgang

3

Thank you for your quick reply.

  1. I used git clone. I have version 24.2
  2. Yes, I have installed srnapipe.
  3. I have Ubuntu 24.04.3 LTS.
  4. Not yet.

Thank you for your help.

4

I cannot reproduce your issue fully. The installation via the suite does indeed not install the conda dependency, but I could readily install the missing conda env via “Manage Dependencies” (I looked for MiModD, ticked the box next to it, went to the bottom of the page and clicked Install).

Alternatively, you can install the three regular repos `mimodd_main`, `mimodd_aln` and `mimodd_snpeff` separately and this will auto-install the conda dependency for you. Just make sure you let the first of these three installs run to completion to avoid parallel conda installations into the same environment, which will typically break things.

For your local instance you can also switch to the terminal or log file (depending how you configured Galaxy) and monitor what’s happening when you’re installing a tool. Maybe that gives you a hint of what’s going on.

5

Thank you for your help. I was following the same steps as you to install the dependencies via Manage Dependencies, but in my case it wasn’t working and I still can’t figure out why. I followed your advice and downloaded the three repos (mimodd_main, mimodd_aln, and mimodd_snpeff) separately. They seem to have finished downloading without any issues, but I haven’t run any of the MiModD tools yet. Hopefully they run without any errors once I tried them. I appreciate your help.