Convenience tools/functions for challenges and benchmarking on Synapse.org
Project description
📖 Documentation: https://sage-bionetworks-challenges.github.io/cnb-tools
👾 Source code: https://github.com/Sage-Bionetworks-Challenges/cnb-tools
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
To fully utilize cnb-tools, you must have a Synapse account and
provide your credentials to the tool. To do so, create a .synapseConfig
file in your home directory, and enter the following:
[authentication]
authtoken = "YOUR PAT"
Generate a new Synapse Personal Access Token (PAT) with all token
permissions enabled, then copy-paste it into authtoken
. Save the file.
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.
Verify the installation with:
cnb-tools
License
cnb-tools is released under the Apache 2.0 license.
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