-
Notifications
You must be signed in to change notification settings - Fork 420
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Add data manager for pangolin-data #4633
Add data manager for pangolin-data #4633
Conversation
This is a data manager for the pangolin-data repository used for the pangolin tool. As discussed with @wm75 each data source for pangolin should be managed separately - this just handles the Data tables produced by this DM:
|
@pvanheus I cannot currently planemo serve the DM so presumably there's something wrong (name or ID mismatch between the different DM/data table files, or something along these lines) still. Or is that not a problem for you? |
It works for me. When I am in the top level directory, then |
works now :) |
In the meantime, I have started working on version 4.1.1 of the pangolin wrapper, which will already offer your new data tables. So before we merge this one here, I'd like to test the use of these tables on the pangolin tool wrapper side. Should be done tomorrow hopefully. |
I do appreciate your hard work on this @pvanheus !
You will still have to turn the selected version into a github download link and all that, but you'll have a direct source of truth for available versions and their min requirements on the pangolin and scorpio side of things. |
Populating the options from a csv file is somewhat an undocumented hack maybe atm (see galaxyproject/galaxy#14324) but in the very worst case the data manager help would have to tell users to run a csv to tabular conversion first on the downloaded file. |
@wm75 please have a look at the new version of the DM PR. |
I've changed the requirements a bit, but looks good to me. Personally, what I would do is decrease the nesting of the interface a bit by presenting three top-level options per data source: |
data_managers/data_manager_pangolin_data/data_manager/pangolin_data_dm.py
Outdated
Show resolved
Hide resolved
data_managers/data_manager_pangolin_data/data_manager/macros.xml
Outdated
Show resolved
Hide resolved
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Really cool, thanks!
Just tiny things left to do here.
data_managers/data_manager_pangolin_data/data_manager/pangolin_data_dm.py
Outdated
Show resolved
Hide resolved
data_managers/data_manager_pangolin_data/data_manager/pangolin_data_dm.xml
Outdated
Show resolved
Hide resolved
One more minor thing: I just noticed that pangolin-data/-assignment version 1.2.133 cannot be installed because the github release tags for them are |
My goodness! pangolin-data versions that look like PANGO lineages. I had a look over on Github and its a very confusing situation: The version is called v1.2.133 in the comment and v1.2.133.1 in the release. Since its such an old release, I'd ignore it except it gets included if people select to download all versions (and then causes an error). |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
This was a tough journey, but the result looks great to me!
Thanks @pvanheus!
FOR CONTRIBUTOR: