Marius van den Beek

Allow type_source to reference a collection input in a repeat

2

I was reviewing the local-only commits I had on our prod server, this one allows `type_source="inputs_0|input"` for ``` ``` The current workaround would be to create one static input, but...

[RFC] Link datasets w/ extension into working directory

10

Another PR in the series of "It's possible, but is it a good idea?" I'd appreciate any feedback (particularly about these points): - should we do the symlinking on the...

Tweak tool form building performance

3

Some performance tweaking to deal with very slow form building of the apply_rules tool on main. This is based on those 2 stack frames (these are pretty much exclusively what...

Add perl dependency for tools using perl

2

Fixes https://github.com/galaxyproject/galaxy/issues/12603. Also need to add new tool versions to safe udpates (Please replace this header with a description of your pull request. Please include *BOTH* what you did and...

## What did you do? - Allow retrying metadata on dataset that is used as job input This should be fine so long as the state is failed_metadata and we're...

Render previews of notebooks

4

Heavily inspired by https://github.com/galaxyproject/SARS-CoV-2/blob/03a07fd6f519e91806084847eec1b9b159095b8d/.vuepress/components/JupyterNotebook.vue, which we could probably mount directly instead of doing it like this. I think we'd probably also want to defer loading of the additional dependencies. If...

Probably doesn't work anyway. If migrations are needed they should be done on older Galaxy releases. Includes https://github.com/galaxyproject/galaxy/pull/9491

This uses the chardet library, but overwrites any guessed encoding with utf-8 if no UnicodeDecodeError is raised. This also makes the is_binary check more stringent, allowing sniffing of datasets with...

This is a WIP that addresses a couple of problems with the involucro based build at the moment. The build process is: - Stage 1 installs target packages using miniconda...