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usegalaxy-eu / project-ideas

A collection of project ideas suitable for Master and Bachelor students
MIT License
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Advanced CLI program to schedule scientific workflows across Europe #17

Closed bgruening closed 2 years ago

bgruening commented 4 years ago

Advanced CLI program to schedule scientific workflows across Europe

Supervisor: Björn Grüning For degree: Bachelor/Project Status: Open/In progress/Completed (assigned to ...) Keywords: workflows, Galaxy, python, REST-API

Global context

Galaxy is one of the biggest bioinformatics open-source projects around and it provides access to HPC and Cloud resources for hundreds of thousands of researchers. Galaxy is usually used via a GUI to schedule workflows. In this thesis, a light-weight but powerful CLI should be developed to easily schedule workflows and get the workflow status.

Project context

In this project, a tool should be developed that interfaces with the RESTful API of Galaxy and schedules jobs and workflows. Smart autocompletion should be integrated to automatically guide the user to missing parameters. Moreover, a fancy status report should be printed to the console, realtime updates would be great as well.

Objectives of the project

Create a CLI to Galaxy to submit workflows and jobs of arbitrary size and report back to the user the status.

Proposed agenda for the project

  1. get familiar with the RESTful API of Galaxy
  2. submit a workflow and tools via Python to Galaxy
  3. get familiar with the python module click or similar libraries, especially the autocompletion feature
  4. implement a workflow run feature
  5. implement access to reports of the started workflow(s)

Prerequisites

Further reading and useful links

simonbray commented 2 years ago

Done (by me, not a student, whoops :))