Getting Started

Dependencies

This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results:

• Python >=3.8 or <3.10
  • pip install -r requirements.txt
• bedtools
• R 4.2.2
  • renv::install()
  • Follow instructions here to install synapser
• Java > 8
  • For mac users, it seems to work better to run brew install java
• wget
  • For mac users, have to run brew install wget

Installation

PyPi

The aacrgenie package is available from PyPI. It can be installed or upgraded with pip.

pip install aacrgenie

Local

Source code and development versions are available on Github. Installing from source:

git clone https://github.com/Sage-Bionetworks/Genie.git
cd Genie

Install the packages locally.

pip install -e .
pip install -r requirements.txt
pip install -r requirements-dev.txt

You can stay on the main branch to get the latest stable release or check out the develop branch or a tagged revision:

git checkout <branch or tag>

Configuration

Configure the Synapse client to authenticate to Synapse.

1. Create a Synapse Personal Access token (PAT).

2. Add a ~/.synapseConfig file with the following information:

   [authentication]
   authtoken = <PAT here>
   

3. OR set an environmental variable

   export SYNAPSE_AUTH_TOKEN=<PAT here>
   

4. Confirm you can log in to synapse in your terminal.

   synapse login