encode-dcc / regulome-encoded

Temp repo for regulome development

Regulome DB

Running app using docker compose

1. Running RegulomeDB using docker compose

• Make sure you have docker compose (https://docs.docker.com/compose/install/) installed. Build the image regulome:

  • docker compose build

• Run regulome:

  • docker compose up

• The app will be running at http://0.0.0.0:6543.

• Stop and remove containers, networks:

  • docker compose down

2. Frontend development using docker compose

• In Docker Desktop, find the running docker compose (should be named as "regulome-encoded"), there will be one docker container runing inside. Select the "CLI" to open the terminal:

  • npm run dev

• The above command runs continually in the terminal window and watches for changes in Javascript and SCSS files, rebuilding the bundles as you make changes.

3. Running test using docker compose

• Choose the regulome service and run the specific test command, for example:
  • docker-compose run regulome npm test

Creating a demo machine

• Install dependency boto3 first then deploy:

  pip3 install boto3
  python src/encoded/commands/deploy.py --profile-name regulome

• The demo link uses this format: https://[instance_name].demo.regulomedb.org/regulome-search/

• Deploy script help (how to specify name, instance size, etc):

  python src/encoded/commands/deploy.py --help

• For all options, including setting up ES clusters (needed for full production). After indexing (currently 8+hrs) the machine can be downsized at AWS to an m4.2xlarge, unless you are planning to submit significant data to it.

Linting your code within your code editor

To set up linting with Sublime Text 3 or Visual Studio Code, first install the linters:

pip3 install flake8
npm install -g eslint
npm install -g eslint-plugin-react

⚠️ Note: You don't have to use Sublime Text 3 but you must ensure that linting in your editor behaves as it does in Sublime Text 3.

Sublime Text 3

After first setting up Package Control (follow install and usage instructions on site), use it to install the following linting packages in Sublime Text 3:

• sublimelinter
• sublimelinter-flake8
• SublimeLinter-contrib-eslint (Sublime linter eslint instructions)
• babel (Babel instructions)

Sublime Linting with pyenv To get Sublime to lint Python code using pyenv you must add the python version and paths and python_paths to your Sublime Linter Preferences. In Sublime Text, navigate to the user linter preferences:

• Sublime Preferences -> Package Settings -> Sublime Linter -> Settings-User

• Add the following (modify existing preference settings file or add this entire JSON object below if the file is blank):

{
    "user": {
        "@python": 3.8,
        
        "paths": {
            "linux": [],
            "osx": [
                "/Users/YOURUSERNAME/.pyenv/versions/3.8.10/bin/",
                "/Users/YOURUSERNAME/.pyenv/versions/2.7/bin/"
            ],
            "windows": []
        },
        "python_paths": {
            "linux": [],
            "osx": [
                "/Users/YOURUSERNAME/.pyenv/versions/3.8.10/bin/python3",
                "/Users/YOURUSERNAME/.pyenv/versions/2.7/bin/python"
            ],
            "windows": []
        }
    }
}

• Restart Sublime

Visual Studio Code

Go to the Visual Studio Code marketplace and install these extensions:

• ESLint
• Python
• Sass

Check versions and linting

Versions

• python3 --version returns Python 3.8.10 (or variant like 3.8.x)
• node --version returns v10.15.0 (or variant like v6.x.y)

Linting check

• Python: Open Sublime, make a change to a Python file, make an intentional syntax error (no : at the end an if evaluation). Warnings and errors should show on the left side of the line.

• JavaScript: Make a syntax error, or style error, in a JS file. Warnings and errors should show on the left side of the line.

regulome-encoded's Issues

User Request - Variant_id format

Would it be possible to have RegulomeDB accept SNP Ids in Variant_Id format as in GTEx data. Conversion of it to RSID format for large amount of data is computationally expensive.

[email protected]

Feature Request for high-throughput

Can you release a script that can score all variants in a VCF as part of a high-throughput pipeline?