README-local-install.md

Genomic Data Services

Installation Requirements

• python 3.8 (locally 3.9 and 3.10 work as well)
• postgres (only for RNAGet?)
• elasticsearch (5.6 currently)

Application Installation

1. Create a virtual env in your work directory. This example uses the python module venv. Other options would also work, like conda or pyenv

   cd your-work-dir
   python3 -m venv genomic-venv
   source genomic-venv/bin/activate
   

2. Clone the repo and install requirements

   # Make sure you are in the genomic-venv
   cd genomic-data-service
   pip3 install -e .
   

3. Download our machine learning models and other files needed

   python3 ./utils/download_files.py
   

4. Run the application:

   make run
   

   It will be available on port 5000.

5. (Optional) Run the indexer (independent of flask application):

• if redis not running, start redis first:

  brew services start redis
  

• in separate windows, with virtualenv

  # start local ES
  python3 ./utils/dev_server/dev_server.py
  make worker
  make flower
  make index
  

• if you just want to index a small number of files for local install, run make index_local instead of make index.

• Monitoring via flower will be available on port 5555 (localhost unless otherwise set).