Convenience tools/functions for challenges and benchmarking on Synapse.org

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📖 Documentation: https://sage-bionetworks-challenges.github.io/cnb-tools

👾 Source code: https://github.com/Sage-Bionetworks-Challenges/cnb-tools

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cnb-tools is a set of tools and commands that provides an interface for managing crowd-sourced challenges hosted on Synapse.org, including but not limited to, DREAM Challenges.

Requirements

• Python 3.10+
• Synapse account

To fully utilize cnb-tools, you must have a Synapse account and provide your credentials to the tool. First, generate a Synapse Personal Access Token (PAT) with all token permissions enabled.

Next, run the following command, then follow the prompts to enter your Synapse username and PAT:

synapse config

This will create a .synapseConfig file in your home directory. For security, we recommend updating its permissions so that other users on your machine do not have read access to your credentials, e.g.

chmod 600 ~/.synapseConfig

Installation

For best practice, use a Python environment to install cnb-tools rather than directly into your base env. In our docs, we will be using miniconda, but you can use miniforge, venv, pyenv, etc.

# Create a new env and activate it
conda create -n cnb-tools python=3.12 -y
conda activate cnb-tools

# Install cnb-tools using pip
pip install cnb-tools

ⓘ NOTE

cnb-tools builds off of the Synapse Python Client — by installing cnb-tools, you will also be installing synapseclient.

→ Read its docs.

Verify the installation with:

cnb-tools

Running With Docker

If you rather not install cnb-tools onto your machine, you may still use it via Docker! The package and list of versions are available here.

To provide your Synapse credentials to the Docker container, you must first create a file with your Synapse PAT as the SYNAPSE_AUTH_TOKEN environment variable:

SYNAPSE_AUTH_TOKEN=<YOUR PAT>

The docker run command will look something like this, assuming the file is named ~/.synapse-config:

docker run --rm \
  --env-file ~/.synapse-config \
  ghcr.io/sage-bionetworks-challenges/cnb-tools \
  COMMAND [ARGS]

License

cnb-tools is released under the Apache 2.0 license.