We’re in the middle of setting up a new Galaxy server (18.09) and currently installing tools - mixed ToolShed and locally developed code.
Quite a lot of our tools are currently failing with error:
Conda dependency seemingly installed but failed to build job environment.
This includes BCFTools, GATK (3.x), and others. Looking through the manage dependencies panel, the ones with issues often have multiple dependency requirements, with Conda as the resolver and separate environment paths listed. Other, working tools with multiple requirements via conda give the same mulled-v1-HASH environment path for all of them. Now, we don’t have the mulled beta enabled right now, and I’m not sure we ever did, so I don’t know how these were sourced. We also aren’t caching the dependencies, although maybe we need to.
Has anyone seen this behavior, or have any troubleshooting suggestions? Is there a latency factor here - could it fail due to time taken to build the env across filesystems?