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Tools

Install the following tools needed for AMPPD development:

APIs

We use the following API for development, the relevant dependencies are included in pom.xml of the corresponding projects:

  • Spring Boot
  • Jersey (used by blend4j)
  • Hibernate/JPA
  • JUnit
  • TestNG (used by blend4j): if you are using Eclipse, you need to download the plugin 
  • Log4j
  • Liquibase

Repositories

Clone the following projects for AMPPD at AMP Github home

  • amppd:
    • the main AMPPD app
    • In Eclipse, you can run the app with Maven clean or as Spring Boot App
    • In Eclipse, you can run the tests with Maven test or as JUnit test
  • galaxy:
    • currently serves as the backend workflow engine for amppd, also used for workflow UI's in the pilot project
    • To run it, go to the root directory where galaxy is installed, and type "./run.sh"
    • Note: Galaxy currently requires Python 2.7 on Linux to run
  • blend4j:
    • a java library providing APIs to interact with Galaxy REST endpoints
    • In Eclipse, you can run the tests with Maven test or as TestNG test

Other projects under AMP Github home are not under active development. They serve either as dependencies or references. Download them if you want to view the source code.

Galaxy Dependencies

Below are a list of tools, command line and python, that need to be installed independently to run workflows.  

  • jq
  • python3
  • boto3
  • spacy (pip)
  • pyscenedetect (pip)
  • pytesseract (pip)


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