Missing module error at Galaxy instance

Question

[Ibrahim Tanyalcin]

I have a Galaxy installation at a cluster that makes use of default python 2.7. I can see that there are 2 symlinks called python2 and python2.7 that maps to a python binary inside /galaxy/.venv/bin and calling it with --version returns 2.7.14

I recently installed a tool using tool.xml that has the following directive:

<configfiles>
  <inputs name="inputJSON" filename="myConfig.json" data_style="paths"></inputs>
<configfiles>

The above directive tells galaxy to parse the entire UI from XML and create a JSON representation of the user choices, which is then passed to a perl script.

When I ran the tool I got the following error:

ImportError: No module named xml.dom.minidom

Since the tool and the wrappers are written in node and perl, I am guessing this has something to do with galaxy dependencies that is required to parse the xml directive above.

I checked the default python from $PATH and it's version is 2.7.14 as well. When I go to /usr/lib64/python2.7 or /usr/lib64/python I can see that there is a folder structure xml -> dom -> minidom.py. So it means I already have this module installed.

Next I went to galaxy/.venv and I see there is a folder called lib and another called lib64 which points to lib itself. Inside the lib there are many python scripts that are symlinks inside /usr/lib64/python2.7/. For example types.py maps to /usr/lib64/python2.7/types.py .

At this point I have 2 questions:

1. Shall I create a folder symlink called xml inside galaxy/.venv/lib that maps to /usr/lib64/python2.7/xml ? Would that be sufficient ?
2. Shouldn't these dependency symlinks be refreshed when galaxy is restarted? Because when I restart galaxy, I still get the same error, meaning galaxy is still not aware that this module exists.

Answer 1

[Ibrahim Tanyalcin]

Turns out, Galaxy 18.09 does NOT place the JSON representation of the inputs in the working directory, but places it inside the parent of the working directory. And instead of the error from your wrapper, you see missing module error from the python script that has called your wrapper. See full explanation here