Question: Error when running local Galaxy tool
0
gravatar for giulia.pasquesi
4 months ago by
giulia.pasquesi0 wrote:

I am trying to run the program TEdenovo (from installed from the Tool Shed) , but I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/Users/julia/Desktop/shed_tools/toolshed.g2.bx.psu.edu/repos/vmarcon/repet_tedenovo/baea09e6722b/repet_tedenovo/TEdenovo_lite.py", line 10, in <module> from commons.core.seq.FastaUtils import * ImportError: No module named commons.core.seq.FastaUtils

I tried to debug it, but things look very different (I also installed the REPET package, that is required.).

Thank you so much in advance. Giulia

software error • 129 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson23k • written 4 months ago by giulia.pasquesi0
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The error reports a missing dependency. Log into the Tool Shed and send the repository owner a message about the issue ("Repository Actions"). Repositories not owned by devteam or iuc need to have issues addressed by the original repository owner unless they grant permissions to the IUC (or you, if interested).

Technical notes: The tool needs an update (examples). How dependencies are included natively and managed during tool installs have changed within Galaxy itself since the tool was published. Review the deprecation notices in the release notes for details, in particular for Galaxy release 17.01.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson23k
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