updated humann2 data manager and regroup

[bernt-matthias]

• downloads utility function
• enable the use of the utility function again

probably this needs some improvement. since I did not work with data managers I'm not sure if this will work. It would be nice if someone could give me some links where I could start reading. In particular: how to test the data manager and the tool together.

[bernt-matthias]

https://bitbucket.org/biobakery/humann2/src/687004f21924e4cffb215b49d49ba29b5490e41b/humann2/tools/better_regroup_table.py?at=default&fileviewer=file-view-default there also seem to be updated versions of some scripts.

[bebatut]

Thanks @bernt-matthias

Looks like they are working on new scripts... But there is no new tags or release yet.
For the regroup tool, I disable the options because in the command-line help, they remove them...

To test the data manager, I usually:

• Push it on the TTS with my account there
• Launch a Galaxy Docker container with TTS installation enable
• Install the data manager from the TTS in my instance in container
• Test it and start the loop
  • Fix it
  • Push to the TTS
  • Update on the container

I will test it also

[bernt-matthias]

I'm struggling with pushing to the TTS. I have tried to follow http://planemo.readthedocs.io/en/latest/writing_appliance.html#publishing-to-the-tool-shed

• I have registered
• added the key to ~/.planemo.yml
• planemo shed_lint --tools
• changed the repository URL in .shed.yml to https://github.com/bernt-matthias/tools-iuc/tree/master/data_managers/data_manager_humann2_database_downloader
• planemo shed_create --shed_target testtoolshed does apparently nothing (no output and I can not find anything in the TTS)

[shiltemann]

just to double-check: did you change the owner in the .shed.yaml file from iuc to your own username? and there is also nothing under "repositories I own" in TTS? (only repos with valid tools will show up in the main tool search) ..as an alternative you could also try using planemo shed_update with the --force_repository_creation parameter as well