nmdpbioinformatics/phycus repository overview

⁠Haplotype Frequency Curation

Service to help curate Haplotype Frequencies.

⁠Development Overview

⁠Pre-requisites:

• JDK 8⁠
• Apache Maven⁠
• Docker⁠

⁠Build the application

mvn clean package

⁠Setup Database

The project is setup to use mysql Docker instance for local development.

cd db/
docker-compose up -d

The phpMyAdmin page should be available at http://localhost:9999/⁠. For Windows, you will need to use the IP of the docker VM instead of localhost. You can retrieve the IP with docker-machine ip. Usually it's 192.168.99.100. Login with hfcus_user user and hfcus_user1 as password.

Use docker-compose stop and docker-compose rm to stop and remove the db containers.

⁠Run the application

⁠Special step on windows

On Windows, you need to start the server using the IP address Docker has assigned. Use docker-machine ip to retrieve it. You'll use it to replace localhost in jdbc:mysql://localhost:3306/hfcusdb when you start your server. (See the command below.)

⁠Starting the application

Start your server as a simple java application
Check your JDK version with java -version

With Java 8:

 java -jar target/service-haplotype-frequency-curation-0.0.1.jar

With Java 8 on Windows:

 java  -Dspring.datasource.url="jdbc:mysql://your-ip-address-here:3306/hfcusdb" -jar target/service-haplotype-frequency-curation-0.0.1.jar

With Java 9:

java --add-modules java.xml.bind -jar target/service-haplotype-frequency-curation-0.0.1.jar

You can view the api documentation in swagger-ui by pointing to http://localhost:8080⁠

⁠Using the service

See client/⁠ directory for examples on using it from various languages. Eg. for Perl⁠

⁠Read the User Guide

See docs/⁠ directory for a user guide and examples of how the service is used in practice.