Deepvariant tool installation error on local Galaxy

usegalaxy.eu support
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1

Hello!
I am running a local instance of Galaxy (build 22.05). I installed the latest version of Deepvariant (1.4.0+galaxy0) which installed without any errors. However, when I try to run Deepvariant on BAM files output from HISAT2, the error “Fatal error: Exit code 127 ()” comes up. Further, it says that the tool generated the following error: “line 9: run_deepvariant: command not found”.
When I look at the backend to see what process Galaxy is going through, even after installation of the tool, the following line keeps repeating on the command line interface:

uvicorn.access INFO 2022-12-22 13:43:26,629 [pN:main.1,p:100965,tN:MainThread] 127.0.0.1:58158 - “GET /api/tool_shed_repositories?name=deepvariant&owner=iuc HTTP/1.1” 200

I don’t understand this error. Could someone please help me out?

I am running the same job on Galaxy.eu server and it is running (for a few hours now) but in the local instance in errors out pretty much instantly.

Thanks!

2

Hello, I can’t give a full answer but I can maybe guide you in the right direction and maybe someone that can give a better answer will reply.
Given the error it looks like deepvariant is not installed (not found). The tool is using a “docker tool dependency”, in other words it needs a container where deepvariant is installed. If you have not checked this yet then I think this is the place to start. Below two links where you may find some more information.

https://docs.galaxyproject.org/en/master/admin/special_topics/mulled_containers.html

The requirement can be seen here:

3

Thank you @gbbio. I will try it out.