search

usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
0 stars 0 forks source link

HMMER3 tools not working #76

Closed kjetilkl closed 1 year ago

kjetilkl commented 1 year ago

A user tried to run the tools hmmsearch and hmmscan, and these jobs have now been stuck in a "queued" state in Galaxy for 2 days. (The jobs have not been submitted to Slurm yet). I believe the problem is that the tool relies on old-style Tool Shed dependencies and the required package could not be found in Conda.

kjetilkl commented 1 year ago

The tool requires the package "hmmer" in version 3.1b1, which is not present in BioConda. But version 3.1b2 is available, so I tried to use that one instead. I found a pre-made container for this package in BioContainers (http://datacache.galaxyproject.org/singularity/h/m/hmmer:3.1b2--3), which I downloaded to usegalaxy.no. Then I used a new script I had made to find the correct name to use for the container based on the requirements in the tool wrapper, and I made a symlink with this name that pointed to the container file. Both tools ran successfully afterwards on test data that came with the tool wrapper.

I have notified the user via email.