bioforklift 0.4.0

Package for handling bioinformatics data automations between data sources

bioforklift

It is highly recommend to serve the documentation locally, as the instructions here are not as thorough as the documentation.

Getting Setup

Installing bioforklift

To install bioforklift, run pip install bioforklift

Using the latest unpublished version

This project uses poetry for project management

If you don't have poetry present, please install it with: pip install poetry

Then run poetry env activate which will create your environment: poetry env activate

Next, install the dependencies listed in poetry.lock utilizing: poetry install

The dependencies will be installed based on the locked versions in the poetry.lock file, since I already ran poetry install and pushed the lock file. For more information on poetry, read here: https://python-poetry.org/docs/basic-usage/

Finally, re authorize your gcloud authentication. This obtains your credentials via a web flow and stores them in 'the well-known location for Application Default Credentials'. Now any code/SDK you run will be able to find the credentials automatically. This is a good stand-in when you want to locally test code which would normally run on a server and use a server-side credentials file. gcloud auth application-default login

Overview