rna_tools: Add DoRiNA data source tool definition.

[rekado]

Add a basic data source tool definition for the public DoRiNA
deployment. When accessed with a GALAXY_URL parametre, DoRiNA offers a
link back to the provided Galaxy instance enabling it to fetch the
results in tabular form.

[bgruening]

@rekado thanks a lot!
Could you please add data_source.py to this repository. I think this was one error we encountered during testing.

[rekado]

Isn't this part of any Galaxy deployment? I did not write the code in data_source.py and it appears to be used by other data sources as well.

[jmchilton]

@bgruening is correct - it needs to live beside the tool. If you look at the tools in Galaxy they are all in folders that also contain data_source.py files (I think there is just one such folder actually).

[rekado]

Okay then. I'll add data_source.py tomorrow then. (I wonder why it works in our Galaxy installation, but I can't investigate right now.)

[TorHou]

@rekado thank you a lot 👍 I'm very glad you did this so quickly. I hope the de.NBI members will take notice 😏
If you install the tool from the toolshed it will put it in a different shed-tools directory.. with no data_source.py present. It shouldn't work if you delete dorina from you tools/data_source directory and just use the toolshed version.

[rekado]

I added data_source.py, though I'm not sure if that's sufficient (I didn't have the time to set up the dorina data source as it would be when installing from the tool shed).

I could not find any license headers on data_source.py and I don't know where upstream for this file would be. Before merging I would like to make sure that data_source.py is in fact available under a free software license.

(Do you want me to add license headers to dorina.xml? As part of webdorina it is released under GPLv3+.)

[blankenberg]

@rekakdo the file located at tools/data_source/data_source.py in the Galaxy distribution is Academic Free License version 3.0: https://raw.githubusercontent.com/galaxyproject/galaxy/dev/LICENSE.txt

Although, ideally, we should probably build a separate dependency package containing this python script and attempt to decouple it from the Galaxy code as much as possible. I wouldn't consider that a blocker at this point, however.

[blankenberg]

Also, I do not think you need to add that license to the xml, the xml doesn't contain any part of the dorina code.

[rekado]

Well, as the author of dorina.xml I can publish it under dual licenses to make it possible to combine it with the AFL3.0 in the context of Galaxy and with my preferred license, the GPLv3+, so this is not an insurmountable problem :)

[bgruening]

@blankenberg is it ok for you to put data_source.py into a IUC repository - package_galaxy_data_source_0_1?
@rekado do you want to add anything? Otherwise I will merge this and add a tool dependency as soon as I have created the IUC repository for data_source.py.

[rekado]

I have nothing more to add. The last commit adds license notes for both files in a separate LICENSE file, indicating that for the XML file a license exception to combine with Galaxy is granted. (AFL and GPL are not compatible, unfortunately, so I had to make this dual-licensing explicit.)

[bgruening]

Great! Thanks a lot!