Question: Galaxy Tool Unit Test
0
gravatar for leshin
12 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 • 337 views
ADD COMMENTlink written 12 months ago by leshin0
3
gravatar for Devon Ryan
12 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 12 months ago by Devon Ryan1.9k

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

ADD REPLYlink modified 12 months ago • written 12 months ago by leshin0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 110 users visited in the last hour