PathoGin is a tool designed for analyzing and identifying pathogenic sequences from genetic data. It streamlines the process of pathogen detection by providing an efficient workflow for bioinformatics research, making it easier to analyze, test, and deploy the application across different environments. The tool is geared towards researchers and developers looking for a robust, automated solution to handle pathogen-related genetic data processing and analysis.
Follow these instructions to get a local copy of the project up and running for development and testing purposes. Check the deployment section for notes on how to deploy the project in a production environment.
Ensure you have the following installed:
- Docker
- GNU Make
Use the following commands to manage the application:
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Run build and tests
Compiles the project and runs the test suite:make all
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Build the application
Creates a build of the application:make build
-
Run the application
Executes the application locally:make run
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Create DB container
Spins up a Docker container with the database:make docker-run
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Shutdown DB container
Stops and removes the running Docker container for the database:make docker-down
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Run DB Integration Tests
Executes database integration tests:make itest
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Live reload the application
Watches for file changes and reloads the application automatically:make watch
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Run the test suite
Runs all tests in the project:make test -
Clean up
Removes the binary from the previous build:make clean