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Question: Error when running local Galaxy tool
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gravatar for giulia.pasquesi
14 months ago by
giulia.pasquesi • 0
giulia.pasquesi • 0 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 • 367 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by giulia.pasquesi • 0
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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