Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Task Execution Service (TES) API specification.
proTES is an proxy-like implementation of the GA4GH TES OpenAPI specification based on Flask and Connexion built for distributing TES tasks over different TES service instances.
proTES is part of ELIXIR, a multinational effort at establishing and implementing FAIR data sharing and promoting reproducible data analyses and responsible data handling in the Life Sciences. Infrastructure and IT support are provided by ELIXIR Finland at the CSC, the TESK service is being developed and maintained by ELIXIR UK at the EBI in Hinxton, and proTES itself is being mainly developed by ELIXIR Switzerland at the Biozentrum in Basel and the Swiss Institute of Bioinformatics.
Ensure you have the following software installed:
- Docker (18.06.1-ce, build e68fc7a)
- docker-compose (1.22.0, build f46880fe)
- Git (1.8.3.1)
Note: These are the versions used for development/testing. Other versions may or may not work.
Create data directory and required subdiretories
mkdir -p data/db data/output data/tmpClone repository
git clone https://github.com/elixir-europe/proTES.git appTraverse to app directory
cd app- Via configuration files:
vi wes_elixir/config/app_config.yaml
vi wes_elixir/config/override/app_config.dev.yaml # for development service
vi wes_elixir/config/override/app_config.prod.yaml # for production server- Via environment variables:
A few configuration settings can be overridden by environment variables.
export <ENV_VAR_NAME>=<VALUE>- List of the available environment variables:
| Variable | Description |
|---|---|
| MONGO_HOST | MongoDB host endpoint |
| MONGO_PORT | MongoDB service port |
| MONGO_DBNAME | MongoDB database name |
| MONGO_USERNAME | MongoDB client username |
| MONGO_PASSWORD | MongoDB client password |
| RABBIT_HOST | RabbitMQ host endpoint |
| RABBIT_PORT | RabbitMQ service port |
Build container image
docker-compose buildRun docker-compose services in detached/daemonized mode
docker-compose -f docker-compose.yaml -f docker-compose.dev.yaml up -d # for development service
docker-compose -f docker-compose.yaml -f docker-compose.prod.yaml up -d # for production serviceVisit Swagger UI
firefox http://localhost:7878/ga4gh/tes/v1/uiEnsure you have the following software installed:
- curl (7.47.0)
- Git (2.7.4)
- MongoDB (4.0.1)
- Python3 (3.5.2)
- RabbitMQ (3.5.7)
- virtualenv (16.0.0)
Note: These are the versions used for development/testing. Other versions may or may not work.
Ensure RabbitMQ is running (actual command is OS-dependent)
sudo service rabbitmq-server statusStart MongoDB daemon (actual command is OS-dependent)
sudo service mongod startClone repository
git clone https://github.com/elixir-europe/proTES.git appTraverse to project directory
cd app
project_dir="$PWD"Create and activate virtual environment
virtualenv -p `which python3` venv
source venv/bin/activateInstall required packages
pip install -r requirements.txtInstall editable packages
cd "${project_dir}/venv/src/py-tes"
python setup.py develop
cd "$project_dir"Install app
python setup.py developOptionally, override default config by setting environment variable and pointing it to a YAML config file. Ensure the file is accessible.
export TES_CONFIG=<path/to/override/config/file.yaml>Start service
python pro_tes/app.pyIn another terminal, load virtual environment & start Celery worker for executing background tasks
# Traverse to project directory ("app") first
source venv/bin/activate
cd pro_tes
celery worker -A celery_worker -E --loglevel=infoVisit Swagger UI
firefox http://localhost:8080/ga4gh/tes/v1/uiNote: If you have edited TES_CONFIG, ensure that host and port match the values specified in the config file.
Coming soon...
Join us at the 2018 BioHackathon in Paris, organized by ELIXIR Europe (November 12-16)! Check out our project description.
This project is a community effort and lives off your contributions, be it in the form of bug reports, feature requests, discussions, or fixes and other code changes. Please read these guidelines if you want to contribute. And please mind the code of conduct for all interactions with the community.
Development of the app is currently still in alpha stage, and current "versions" are for internal use only. We are aiming to have a fully spec-compliant ("feature complete") version of the app available by the end of 2018. The plan is to then adopt a semantic versioning scheme in which we would shadow TES spec versioning for major and minor versions, and release patched versions intermittently.
This project is covered by the Apache License 2.0 also shipped with this repository.
The project is a collaborative effort under the umbrella of ELIXIR Europe.
Please contact the project leader for inquiries, proposals, questions etc. that are not covered by the Q&A and Contributing sections.