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galaxyproject
A Python library for interacting with the Galaxy API
Ex: Run a workflow in Galaxy that generates a `.bam` output. Galaxy automatically generates a `.bai` file associated with this `.bam` to run IGV etc. For my use case I...
This might also be missing from the Galaxy instance, but it would be really helpful to be able to delete user visualizations through the API/Bioblend.
It would be nice to have a delete_group function for galaxy. In there a reason that this is not implemented -- or is there maybe another way to achieve group...
- [ ] add / remove user from role (needs galaxy implementation first) - [x] add / remove group from role (needs galaxy implementation first) - [ ] undelete role...
Create a `gi.histories.rerun_failed_jobs()` method to rerun all failed jobs in a history. This could be done with the current API but afaics would require a for loop over all the...
Is it possible to share histories with other users using Bioblend? If not, are there suggestions for good ways to do this?
Accessing datasets in a public history (that does not belong to me) is restricted in an inconsistent way. When I try to match datasets using the `show_matching_datasets` function, it throws...
I am getting problems when invoking workflows where optional input file parameters (i.e. the XML tool includes `optional="true"`) are left blank in the workflow. The workflows will either not run...
Include specification of subworkflow steps in PARAM_DICT. Placing here in case people are curious: {STEP_ID: {SUBWORKFLOW_STEP_ID|PARAM_NAME: VALUE, ...}}
Hi everyone, I'm trying to export and download (for backup reasons) multiple histories. With some histories I get an ConnectionRestError and proxyError(see below), other histories just work fine. My code:...
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A Python library for interacting with the Galaxy API