Minor fixes to tool_data_table_conf and related files for clair3 and artic #6790
Conversation
| @@ -2,8 +2,8 @@ | |||
| <tables> | |||
| <!-- Locations of clair3 model folders --> | |||
| <table name="model" comment_char="#"> | |||
| <columns>value, name, platform, path, source</columns> | |||
| <file path="tool-data/model.loc" /> | |||
| <columns>value, platform, sha256, path, source</columns> | |||
There was a problem hiding this comment.
That's very unfortunate, but you cannot change the columns of an existing data table.
You need also a new table name now.
There was a problem hiding this comment.
Just to clarify - the table is not like the one described here - the canonical version of the table is the one described here: #6659 (there was something to create the table before this DM was created, even though it was referenced in the clair3 tool). So this brings the clair3 copy of the data table definition in line with the one made by the data manager.
There was a problem hiding this comment.
Ah ok, I see (was wondering how I had missed this when reviewing the PR for the DM). Then this might work.
Not exactly sure how all the different versions of this file are treated by Galaxy though.
There was a problem hiding this comment.
Not exactly sure how all the different versions of this file are treated by Galaxy though.
This will create problems if someone already installed the version without the fix.
There was a problem hiding this comment.
@bernt-matthias will the problem be there if people installed the tool with the older version of the data table or only for those installing the DM (if, for example, a data table changed after the DM was installled)?
There was a problem hiding this comment.
Yeah, but I guess/hope we can manage to clean things up.
There was a problem hiding this comment.
but @bernt-matthias you'd merge without a version bump then, correct?
There was a problem hiding this comment.
ok, then let's do that. @pvanheus can you undo the two wrapper version bumps and I'll try to sort out the EU data tables?
There was a problem hiding this comment.
It also seems that you haven't captured all the changes from #6796 (which unfortunately has been merged already) in this PR here (which means we cannot overwrite the +galaxy0 version of artic_minion here anymore). Can you please just rebase?
(No harm done with the artic_minion tool since that one always had the correct tool_data_table_conf data :-) but rebasing would still be good to make the situation less confusing. )
| @@ -2,8 +2,8 @@ | |||
| <tables> | |||
| <!-- Locations of clair3 model folders --> | |||
| <table name="model" comment_char="#"> | |||
There was a problem hiding this comment.
the name of the table is clair3_models. Can you update that please?
There was a problem hiding this comment.
same for the artic_minion tool!
|
@pvanheus another question while we're at it: have the model files ever changed their format? |
The model files that are built by the clair3 group (available here) have not changed since October 2021, which is before the release date of any of the versions of clair3 used in Galaxy, so it seems that the model format is very stable and definitely stable across all Galaxy tool releases. |
FOR CONTRIBUTOR: