No module named Galaxy when running an old tool (PeakRanger)

Question: No module named Galaxy when running an old tool (PeakRanger)

9 months ago by

Dear Galaxy Community

I have recently installed PeakRanger from the Toolshed. I struggled a bit because the wrapper is old, the link to download the dependency was not working (in tool_dependencies.xml), and there were a lot of identation problems with the python wrapper called to execute the tool. I fixed everything, but...

Now I am facing a new problem; when I try to run the tool

    Traceback (most recent call last):
  File "/mnt/extStorage/shed_tools/toolshed.g2.bx.psu.edu/repos/modencode-dcc/peakranger/d6b1bb81fa6c/peakranger/ranger_wrapper.py", line 6, in 
    from galaxy import eggs
ImportError: No module named galaxy
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip'
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip'
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip'
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip'
WARNING:galaxy.model:Datatype class not found for extension 'wig, zip'

I have read on forums that is is probably related to PYTHONPATH, but I don't exactly know how to fix it. I am using the most recent distribution of Galaxy with a virtual environment. By default, I dont have a $PYTHONPATH environment variable set up on my system (doing an echo prints nothing).

Thanks in advance for your help!

Sincerely

David

peakranger galaxy python • 378 views

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modified 9 months ago • written 9 months ago by david.roquis • 30

9 months ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Hi David

Have you tried setting "preserve_python_environment = legacy_only" in galaxy.ini ? and list your tool in ~/lib/galaxy/tools/__init__.py : "GALAXY_LIB_TOOLS_UNVERSIONED = [..." (# Tools that require Galaxy's Python environment to be preserved.)

Regards, Hans-Rudolf

ADD COMMENT • link written 9 months ago by Hotz, Hans-Rudolf • 1.8k

9 months ago by

david.roquis • 30

david.roquis • 30 wrote:

Dear Hans-Rudolf

Thank you for your message. I was able to solve the issue in a very unorthodox way. I will describe it here in case some people want to use this tool and face the same problem as I have.

First of all, the link to download the tool in "tool_dependencies.xml" is obsolete. As an admin, I removed this faulty dependency from the admin panel, changed the link in tool_dependencies.xml to a valid one, and re-installed the missing dependency (actually, the peak ranger package) from the admin panel.
The xml wrapper (ranger_wrapper.xml) was calling a python wrapper ranger_wrapper.py) which was causing two issues: a) importError no module named simplejson, b) importError no module named galaxy. I could solve both issues by a) installing simplejson in the galaxy virtualenv (I did so by adding "simplejson==3.13.2" in galaxy/requirements.txt and restarting galaxy) and b) adding the following line "sys.path.append("/mnt/extStorage/galaxy-app/lib")" just below "import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip" in the python wrapper ranger_wrapper.py).

I am quite sure that what I did is kinda messy, but as it solved my issues, I thought it would be a good idea to share it.

Thanks again!

David

ADD COMMENT • link written 9 months ago by david.roquis • 30

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