Launchcontainers: A Python tool for launching containerized analysis on HPC

Title

Launchcontainers: A Python tool for launching containerized analysis on HPC

Leaders

Yongning Lei

email: t.lei@bcbl.eu

Collaborators

No response

Brainhack Global 2023 Event

Brainhack Donostia

Project Description

Launchcontainers is a Python-based program built to automatically launch containerlized MRI processing pipelines. This program takes one config.ymal file, one container.json file, and one subject-session-list.txt file as inputs. Using 1 line of bash command, it will automatically send jobs to HPC clusters regarding your computing demands.

This program is well-suited for multi-subject, multi-scan datasets. And it will save a lot of time if you need analysis your entire dataset with different parameters multiple times.

In future versions, we are trying to add more functionality to this repository so that you can launch all the MRI data analysis pipelines such as Heudiconv, fMRIprep, pRF pipelines and etc. Please keep track of this repo and if you have any questions or suggestions, don’t hesitate to contact Gari: garikoitz@gmail.com and Tiger: t.lei@bcbl.eu

Link to project repository/sources

https://github.com/garikoitz/launchcontainers

Goals for Brainhack Global

• Let more people get to know the advantages of using containers to process MRI data to improve the data availability and reproducibility
• Let beginner level users get familiar with the UNIX operation and git operation
• Add new features to launchcontainer so that it supports more MRI processing pipeline (ie. HeuDiconv, fMRIprep, PRF-analyze)
• Make a better documentation on the project Wiki

Good first issues

1. issue one: https://github.com/garikoitz/launchcontainers/issues/28
2. issue two: https://github.com/garikoitz/launchcontainers/issues/32

Communication channels

https://mattermost.bcbl.eu/bhdonostia/channels/launchcontainer

Skills

• Python intermediate
• Unix intermediate

Onboarding documentation

https://docs.google.com/document/d/1XMmMpp3w7i2o8wVyHv_kUgoTgYVJ7n-qvgIQilfEBEU/edit?usp=sharing

What will participants learn?

• How to use Unix to run python script, navigate to directory, and edit files.
• How to use git to collaborate with other’s, create branch to fix issues, pull-request
• How to use launchcontainers to launch DWI pipeline on SGE, SLURM and local machine

Data to use

I will prepare the converted nifti DWI scan folder in BIDS format and zipped it for use

Number of collaborators

3

Credit to collaborators

Project contributers will be listed in the launchcontainer repo

Image

Type

documentation coding_methods

Development status

2_releases_existing

Topic

reproducible_scientific_methods

Tools

BIDS

Programming language

Python

Modalities

DWI

Git skills

1_commit_push, 2_branches_PRs

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.