galaxy_blast
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peterjc
add blast XML visualizations based on crossbio
This PR will add a Galaxy visualization for BLAST XML files based on http://crossb.io/ and developed by @greenify.
Should fix: https://github.com/peterjc/galaxy_blast/issues/60
@peterjc please not that I have trouble to bind this visualization to a Tool Shed datatype. See more as an inline comment.
You can test this by simply copy this folder into GALAXY_ROOT/config/plugins/visualizations/.
It could be clearer https://github.com/greenify/crossbio/issues/2 but crossbio is also using the MIT licence, so that isn't a problem for adding this :)
Right now TravisCI is failing with AttributeError: 'NoneType' object has no attribute 'endswith' but that looks like a Galaxy problem (maybe we shouldn't track the dev branch?)
Right now I believe the Galaxy Tool Shed still doesn't support visualizations - so how would any end user install this? Just copy the folder under GALAXY_ROOT/config/plugins/visualizations/ as you suggested for me to test this?
Right now I believe the Galaxy Tool Shed still doesn't support visualizations - so how would any end user install this? Just copy the folder under GALAXY_ROOT/config/plugins/visualizations/ as you suggested for me to test this?
Yes, this is the only option I know. Tracking the next-stable branch seems to be better to me.
so how would any end user install this
Easy - put it in core :). I would :+1: a PR to core especially if it also came with the blast datatypes - not sure everyone else would though obviously.
It would also mean we can correct backward incompatible changes to the framework like https://github.com/galaxyproject/galaxy/pull/243 by modifying the plugin itself to match the version of Galaxy it is stored with.
@jmchilton you mean the visualization into core? We would need the datatypes as well to make it work :)
Somehow I missed #243. @peterjc if you use latest :dev you should adopt this before you test it.
If the Galaxy dev / IUC consensus is to move datatypes into the core, we can put the BLAST datatypes back again - which would allow putting this visualization into the Galaxy core too. That seems pragmatic since for now the Tool Shed doesn't support visualizations.
[@greenify this code looks interesting, I want to see it merged here or into the Galaxy core - just unclear where is the best fit right now]
P.S. Looking at https://github.com/galaxyproject/galaxy/pull/243 now...
I think the BLAST datatypes are pretty safe to move to core now. They have a proper definition in blast.py, are used a lot in other tools and have sniffers, even split/merge functions.
If you target dev I can patch the changes for https://github.com/galaxyproject/galaxy/pull/243 in.
It could be clearer greenify/crossbio#2 but crossbio is also using the MIT licence, so that isn't a problem for adding this :)
@peterjc: thanks for bringing up this issue. I will add a proper license file tomorrow once I get back from my short vacation!
It's fantastic that you guys even consider to move this to your core :)
@greenify Adding the code to this repository (galaxy_blast) is under my control, and given @bgruening's endorsement I am positive about this (although I have yet to test it).
Adding it to the main Galaxy core is a bigger hurdle, but has respected advocates pushing for it :)
If that datatype test is erroring or failing on a TS installed datatype - that's a bug. I'll look into that.
@bgruening @peterjc re: the config file datatype: if you go to 'class_to_classes, what is the key used? blast.BlastXml or something else? Try that value inside the <test> element:
<test type="isinstance" test_attr="datatype" result_type="datatype">...the key used...</test>
I've installed the devteam blast types from the toolshed and gotten a visualization to show using the above technique.
@carlfeberhard thanks for looking into it. For me this is: BlastXml.BlastXml and with this it is working. How comes that we have a different id?
Ah - no, sorry: miscommunication. For me the id for the devteam blast xml datatype was BlastXml.BlastXml as well. I just didn't include that in my question to prevent confusion or in case Peter's datatype had a different value.
So it's working with that? If so, good!
Yes, it's working and it looks great!
Just one question, why? ;) I thought it's always the module.Class schema.
The way the registry converts class names to classes using the datatypes registry is less than ideal. It's something I'm working on.
@peterjc can me merge this here? So it get's some attention. Do you plan to merge the datatypes into core?
One of the TravisCI tests was failing, rerunning fixed it so it was probably just an SQLite locking issue.
@bgruening If you're happy to be the contact person for this, then sure - I can merge it. It might be time to move this repository to a team model, perhaps under https://github.com/galaxyproject/ like the IUC owned repositories?
If the Galaxy team agree with pulling datatypes back into the core (after previously moving them to the Tool Shed), then I'm happy to help with that. [Update: That has been done now]