Question: SNPeff datatype not available in Toolshed
0
gravatar for matthias.desmet
2.1 years ago by
Belgium
matthias.desmet150 wrote:

Hi Guys,

When I restarted our Galaxy server I noticed a warning that the snpEff datatype couldn't be loaded. When I tried to reinstall it through the ToolShed I got the following warning:

tool_shed.galaxy_install.install_manager ERROR 2016-01-13 10:46:07,751 No content returned from tool shed repository version request to https://toolshed.g2.bx.psu.edu/repository/get_tool_versions?owner=iuc&changeset_revision=d78b2b2a3388&name=snpeff_datatypes
galaxy.datatypes.registry DEBUG 2016-01-13 10:46:08,681 Loading datatypes from /Shared/galaxy-data/database/tmp/tmp-toolshed-acalpdMDqDZv
galaxy.datatypes.registry DEBUG 2016-01-13 10:46:08,712 Exception importing proprietary code file /Shared/galaxy-data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/snpeff_datatypes/d78b2b2a3388/snpeff_datatypes/snpeff: invalid syntax (snpeff.py, line 22)
galaxy.datatypes.registry ERROR 2016-01-13 10:46:08,757 Error importing datatype module galaxy.datatypes.snpeff: No module named snpeff
Traceback (most recent call last):
  File "lib/galaxy/datatypes/registry.py", line 204, in load_datatypes
    module = __import__( datatype_module )
ImportError: No module named snpeff
galaxy.datatypes.registry DEBUG 2016-01-13 10:46:08,791 Exception importing proprietary code file /Shared/galaxy-data/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/snpeff_datatypes/d78b2b2a3388/snpeff_datatypes/snpeff: invalid syntax (snpeff.py, line 22)
galaxy.datatypes.registry ERROR 2016-01-13 10:46:08,807 Error importing datatype module galaxy.datatypes.snpeff: No module named snpeff
Traceback (most recent call last):
  File "lib/galaxy/datatypes/registry.py", line 204, in load_datatypes
    module = __import__( datatype_module )
ImportError: No module named snpeff

Which leads me to believe there might be something that's going wrong there, since no content was returned.

Any ideas?

Thanks!
M

snpeff toolshed • 610 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson24k • written 2.1 years ago by matthias.desmet150

Are you running a local Galaxy or Cloudman? Which release/development branch are you tracking?

Thanks! Jen, Galaxy team

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson24k

Hi Jennifer,

Thanks for the response!

I'm running a local Galaxy deployment ( release 15.10) on a ubuntu 14.04.3 system. However, I don't really think this matters, since we connect to the public Main Toolshed. If I understand the error correctly, our instance gets an empty response from the Toolshed when trying to download the data, which in turn makes the python script throw the ImportError.

Matthias

ADD REPLYlink written 2.1 years ago by matthias.desmet150
3
gravatar for Dave B.
2.1 years ago by
Dave B.410
United States
Dave B.410 wrote:

Matthias,

That message was due to a python error in the upstream version of snpeff.py. I have now corrected that error, and snpeff_datatypes should work correctly if you update to the latest revision.

ADD COMMENTlink written 2.1 years ago by Dave B.410

Hi Dave,

Thank for the fast response! I installed the latest revision and no more errors so far.

Thanks again!
Matthias

 

ADD REPLYlink written 2.1 years ago by matthias.desmet150
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