cBioPortal Galaxy Connector

Overview

cBioPortal Galaxy Connector is a Python-based application that allows users to export data from cBioPortal to a Galaxy instance. The application processes tab-delimited data, prepares it, and uploads it to a specified Galaxy history.

Features

• Environment Configuration: Configure Galaxy URL via environment variables.
• Data Preparation: Process and prepare tab-delimited data for upload.
• Retry Mechanism: Retry Galaxy instance creation on connection failure.
• File Upload: Upload prepared data to a specified Galaxy history.

Requirements

• Python 3.7+
• pandas
• requests
• fastapi
• uvicorn
• bioblend
• cbioportal-core

Installation

1. Clone the repository:

   git clone https://github.com/jCHENEBY/cbioportal-galaxy-connector.git
   cd cbioportal-galaxy-connector

2. Create a conda environment from the environment file and activate it:

   conda create --name cbioportal-galaxy-connector --file environment.yaml
   conda activate cbioportal-galaxy-connector

3. Run the application:

   uvicorn main:app --reload --host 0.0.0.0 --port 3001

Configuration

Environment Variables

• GALAXY_URL: Specify the Galaxy instance URL.
• LIMIT_IP: Set to true to enable IP filtering (default is false).
• STUDY_DIRECTORY: Path to the study directory (default is /study).
• CBIOPORTAL_URL: URL of the cBioPortal instance.
• CBIOPORTAL_CACHE_API_KEY: API key for cBioPortal cache.

Set the GALAXY_URL environment variable to specify the Galaxy instance URL:

export GALAXY_URL='http://your-galaxy-instance-url'
export PYLONE_API_KEY='your-pyclone-api-key'
export PYLONE_DATA_PATH='/path/to/your/data'
export LIMIT_IP='true'

IP Filtering

The application includes middleware to limit access based on IP addresses. This feature can be enabled or disabled using the LIMIT_IP environment variable.

• When LIMIT_IP is set to true, IP filtering is applied.
• When LIMIT_IP is set to false (default), IP filtering is bypassed.

IP Filtering Rules

• GET /images/{image_name}: Accessible from anywhere.
• DELETE /images/{image_name}: Restricted by IP.
• /export-to-galaxy/: Accessible from anywhere.
• Other endpoints: Restricted by IP.

Allowed IPs and Subnet

• ALLOWED_IPS: List of allowed IP addresses (default is ["127.0.0.1"]).

Usage

1. Ensure the GALAXY_URL environment variable is set.
2. Start the application using the uvicorn command mentioned above.
3. Use the provided API endpoints to interact with the application and export data to Galaxy.

Docker

To build and run the application using Docker:

1. Build the Docker image:

   docker build -t cbioportal-galaxy-connector .

2. Run the Docker container:

   docker run -p 3001:3001 cbioportal-galaxy-connector