First, I'm at a bit of a loss to even describe what's going on, so I apologize in advance for a rambling bug report. Please bear with me! 

The naive_variant_caller tool was failing on our instance with "Failed to resolve dependency" errors on numpy, pyBamParser, and pyBamTools, despite the tool dependencies and their respective dependency packages being installed. 

I attempted to use the "repair repository" action on naive_variant_caller with no success. I then uninstalled naive_variant_caller, package_numpy_1_7, package_pybamparser_0_0_1, and package_pybamtools_0_0_1 and attempted to reinstall naive_variant_caller from scratch, again allowing Galaxy to manage the dependencies.

This time, the dependencies resolved (at least as far as the "Building dependency shell command" messages were concerned), but naive_variant_caller still failed, this time with an import error:

ImportError: No module named pyBamTools.genotyping.naive

Digging around a little I found that the env.sh that was sourced for pyBamTools was looking for an env.sh in another pyBamTools revision directory, but the revision it was looking for didn't exist.

Then I looked in the admin interface and saw that package_pybamtools_0_0_1 and package_pybamparser_0_0_1 were each installed twice; each had both the most recent revision and an older revision with the "updates are available" icon.

At this point I uninstalled naive_variant_caller and all of its dependency packages again. I then installed naive_variant_caller from the toolshed *without* dependency management, and manually installed the required revisions of numpy, pybamparser, and pybamtools. Finally naive_variant_caller started working.

However, naive_variant_caller is now shown in the admin interface as "Installed, missing repository dependencies", and the installed repository page shows that the dependencies are a very strange state (see attached screenshot). That is, the same revision of numpy is listed as installed twice, and the pybamparser and pybamtools dependencies are each listed as simultaneously installed and uninstalled.

Can anyone shed some light on what could be happening and what to do about it? Is there some external way to verify the consistency of a tool and its dependencies?

Thanks!

Cheers,

Brian

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