noah-cli 0.1.0

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Noah

Noah is a bioinformatics project management tool that makes analysis of large datasets reproducible and easy to share.

Features

• A human-readable configuration file
• Automated retrieval of data from public databases
• Managing data, containers, and workflows, all in one place

Installation

The easiest way to install Noah is to use pip:

pip install noah-cli

Quickstart

To get started with Noah, you can use the noah init command to create a new project:

noah init my_project # This will by default create a Git repository in my_project
cd my_project

To add a new dataset to your project, you can use the noah add command:

noah add SRP123456 # ENCSR123ABC, GSE123456, etc. are also supported

You can also add privately hosted datasets:

noah add some_host:my_dataset ftp://ftp.example.com/another_dataset # You can add multiple datasets at once

Datasets are structured as project/experiment@library_type/pipeline_phase, using metadata from public databases or user input. To input metadata manually, you can add extra options to the noah add command:

noah add my_project/my_dataset --project my_project --experiment my_experiment --library_type chip --pipeline_phase raw
noah add SRP123456 --library_type SRX123:chip-input,SRX456:chip-input # Metadata of public datasets can be overridden if specified

To share your project with others, simply push it to GitHub, and they can retrieve the data with the noah install command:

git clone https://github.com/me/my_project.git
cd my_project
noah install

License

Noah is licensed under the MIT license. See LICENSE for details.