bioblend

bioblend copied to clipboard

Workflow with collection fails to execute but works through UI

1

I have a workflow that uses dataset collections, which works through the interface, but produces an error when running through bioblend (latest installable pip version): ``` Traceback (most recent call...

pcm32

Connection aborted using download_dataset

4

Greetings, I am attempting to download datasets from a history using download_dataset with a local instance of Galaxy. This same script used to work perfectly, but now I receive the...

clayfos

HTTP/Socks5 proxy support

1

It would be nice to have more raw access to the `requests`'s kwargs such that we can pass custom things like `proxies=...`.

hexylena

Hello Bioblend developers, I'm here to report that ``` galaxyInstance.histories.show_matching_datasets('history_id') ``` is slow (no results in 20 minutes). @bgruening mentioned this function might not be optimized properly. --- @martenson pointed...

alexlenail

update_group behaviour not as expected

6

The documented behavior of update_group is to substitute previous users. But actually it leads to duplicates of user group associations in the galaxy DB. This has been tested with version...

bernt-matthias

Objects: Wait on jobs instead of datasets

4

In general it is better to wait on jobs instead of datasets when running tools and workflows - in case tools don't have any dataset outputs and to ensure all...

jmchilton

Tool Client improvement

1

https://github.com/galaxyproject/bioblend/blob/c483c871b60821a11bf113bc9bc69a19efa0c355/bioblend/galaxy/tools/inputs.py needs a class for multiple-input fields, deciding if batch mode or not. I can do that, if someone confirms that there is nothing else that already can do that....

kaktus42

Tool Shed Users API

1

Implement client to the Tool Shed users API.

jmchilton

possible race condition

2

My usage of bioblend is perhaps a bit weird, so this may be due to my own extras, but I just got a stack trace and a crash which looks...

cariaso

Support for collecting outputs from tools that produce arbitrary number of outputs at runtime

4

Currently, tools that produce arbitrary number of outputs at runtime (referred to as **A** for arbitrary outputs), making use of the [discover_datasets](https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run) instruction are more complicated to use than regular...

unode