run kmergenie in a local instance

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1

Since Kmergenie is unavailable in public galaxy, I tried to use it in a local instance using the tool derived from (https://toolshed.g2.bx.psu.edu/repository/view_repository?id=2d39d85dc8ccec8e&changeset_revision=2d4b0398cbaf)
However, running this tool generated the following error message:
“/home/trung/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/rchikhi/kmergenie/2d4b0398cbaf/kmergenie/stderr_wrapper.py”, line 47
raise Exception, stderr
^
SyntaxError: invalid syntax

Please advise how to solve this issue. Many thanks

2

Hi @Duc_Trung_Tran

That wrapper was last updated back in 2014. It won’t work on any recent Galaxy release. And, I don’t see a link to the author’s development repository, so there isn’t an obvious contact point.

When choosing wrappers to install on your own server, more recently updated wrappers will work best.

Choices:

  1. Use a different tool/wrapper
  2. Re-write this wrapper
  3. Create a new wrapper
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