make_phylogeny tools fails to run

I tried to use the make_phylogeny tool on but I got this error:

Conda dependency seemingly installed but failed to build job environment.


Hi @Michael_Thon

That’s usually a one-off problem – one particular cluster node had trouble getting set up…

Have you tried a few reruns already? I’m guessing yes but wanted to double check. So if not, please do that first since it might just “go away” :slight_smile:

And, if you share your history, I could test with your data. Or, I can test with the tool test data (or you could, I think you know where to find that at the Tool Shed, yes?). We can create a ticket using that test case so the EU admins know exactly what is going on for a quick fix. It could be some persistent dependency issue that needs a tuneup.

Let me know about the reruns and what you decide to do eg the tool test.

Hi @jennaj
I just tried rerunning it twice and I got the same error. I checked the package in the toolshed and I realized that this is part of Qiime - I thought it was a general tool for phylogeny construction (you don’t expect us to actually read the instructions, do you? :slight_smile: )

In any case, here is a link to the history:

I suppose that even if the data are not formatted properly, that error should not pop up. I cannot find any test data on the toolshed page - would they be in the repository?


Turns out the tool is just at EU for now. And, the author posted a few months ago that Qiime tools are undergoing Galaxy wrapper updates. Maybe the current issue is related. The ticket below will update about that.

The closest alternative tool for now based on your parameters/input is probably → FASTTREE build maximum-likelihood phylogenetic trees

Great, thank you @Michael_Thon

It is a server side issue. I’ve ticketed it here with more details: qiime_make_phylogeny: conda/job configuration issue · Issue #1087 · usegalaxy-eu/infrastructure-playbook · GitHub

I used your history, along with the tool test case. I could change that to just be the tool test and remove your data. Let me know if that matters to you or not. Swapped this out with a new history containing just the our existing test data :slight_smile:

How to find test data:

  1. Load up a tool form
  2. Options → See in Tool Shed (upper right corner)
  3. Click into the ToolShed
  4. Follow the development repository link out
  5. The tool xml file will have the tool tests (to learn which data files were used, and how other options were set)
  6. The directory test-data (usually at the top level, but sometimes nested) will have the actual files. The names will match the tests in the xml. Capture the “raw” link for a file, then paste into Upload tool to get it into Galaxy.
  7. Bonus for EU server only: back on the tool form, use Options → Generate Tour … and while the tour itself is not actually working right now, the test dataset will load up (can throw a warning, but does usually load). The test cases in the tool xml can be reviewed in the Tool Shed directly (“view tip files”) or can just experiment from there with the smaller-but-representative dataset(s). Not always perfect but often enough.

I’m going to next cross-test at the other public servers to double check this isn’t a problem with the tool wrapper directly…