Question: Galaxy Tool Unit Test
0
gravatar for leshin
22 months ago by
leshin0
leshin0 wrote:

I tried to use the run_tests.sh script to test a specific tool installed from toolshed. But I always got errors. For example, I would like to do the unit test on tophat2, so I issued the following command from my Galaxy installation directory:

sh ./run_tests.sh -id toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9

where toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9 is the tool id from the shed_tool_conf.xml file.

The error message I got is:

OSError: No such file /home/galaxyapp/test/galaxy-dist/galaxy/functional.test_toolbox:TestForTool_toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9

The tophat2 tool wrapper does have test part in it.

Can someone help to provide some suggestions? Thank you.

unit test • 684 views
ADD COMMENTlink written 22 months ago by leshin0
3
gravatar for Devon Ryan
22 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

You might find planemo (e.g., planemo test /path/to/a/tool) to be a convenient method for testing. That's what's used for automated testing by the IUC.

ADD COMMENTlink written 22 months ago by Devon Ryan1.9k

Thanks for your information. I will give it a try.

ADD REPLYlink modified 22 months ago • written 22 months ago by leshin0
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