Parameterize and execute notebooks
complete
S
Silky Porpoise
We want to parameterize, (inspect), and execute notebooks using Papermill.
Rob Newman
complete
This is available via custom environments in Data Studios, using the following example YAML:
name: papermill-env
channels:
- conda-forge
dependencies:
- papermill=2.6.0
G
Glacier Goat
Silky Porpoise is your intent to incorporate a parameterized notebook as a step in a nextflow workflow?
Rob Newman
in progress
We are actively working on Custom Environment support in Data Studios.
Rob Newman
Silky Porpoise: This will be resolved by the implementation of Custom Environments (the next Data Studios milestone). In the interim, you can run the following in your Jupyter notebook to install
papermill
:!pip install papermill
With session persistence, this library will always be available once executed in the Data Studio session.
Rob Newman
acknowledged