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galaxyproject / planemo-machine

A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.
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planemo test doesn't work in image #61

Closed jmchilton closed 8 years ago

jmchilton commented 8 years ago

xref #60

Docker Hub has some very fresh images with planemo 0.25.1 that have this same issue - the problem is that planemo uses Galaxy's config/job_conf.xml which has handlers defined that differ in name from the one used by the test framework.

bgruening commented 8 years ago

Urgs. But why is the build-in Galaxy working. This is also using this job_conf.xml isn't it?

jmchilton commented 8 years ago

Yeah - it uses that file - but it has the right handler names. Planemo is using randomly assigned names like planemo28450 for its app name I think. The fix is probably just not to fallback to Galaxy's config - I'll try to get this into planemo 0.26.0.

bgruening commented 8 years ago

Awesome thanks!

bgruening commented 8 years ago

Is there a quick fix? I suppose planemo 0.26 is not planned this week :)

bgruening commented 8 years ago

@jmchilton do you have any time schedule for this. @bebatut is working on new training material and I would like to include a link to a recent working image.

Thanks.

jmchilton commented 8 years ago

I'll release planemo 0.26 with a fix tonight. A quick work around is just not specifying galaxy_root in ~/.planemo.yml.

bgruening commented 8 years ago

Thanks @jmchilton!

jmchilton commented 8 years ago

There were a few problems with the fix last night that preventing me from merging before sleep but it has been resolved I think - I will work on a release today.