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Alliance File Generator

AGR File Generator

Description

This tool creates files from Alliance resources. The tool is built and tested with python 3

Current File Types

  • VCF
  • Disease
  • Orthology
  • Expression

Running Tool Example command

You will want to customize your run by setting these two env variable in the docker-compose.yaml file

 export ALLIANCE_RELEASE='2.3.0'
 export NEO4J_HOST=build.alliancegenome.org

if you only want to generate certain types of files make sure to comment/uncomment the files in the src/agr/app.py file.

Generate container

 make build

generate files

 make run

Generated Files

Files that are generated are located in the docker shared folder. This folder can be found by using the following command:

 docker inspect <container>

Run tests

 make test

##Venv

source venv/bin/activate

##Debug

In order to get comprehensive logging statments for debugging purposes.

export DEBUG=True