Skip to content

FU Berlin Bioinformatik Softwarepraktikum (Projektmanagement) 2020

Notifications You must be signed in to change notification settings

bihealth/edu-swp2020-beacons

Repository files navigation

CUBI Education: SWP Bioinformatik Beacons

The SWP Beacon Project is a Software which allows users to ask for the existence of given variants thereby it uses the Beacon protocol.

Getting Started for v.2.0.0

These instructions will get you a copy of the project and how to get the system running on your local machine for testing purposes.

Prerequisites and Installing

Please clone the repository edu-swp2020-beacon on git and navigate to the edu-swp2020-beacon file:

$ git clone [email protected]:bihealth/edu-swp2020-beacons.git
$ cd edu-swp2020-beacons

The application is running with Python, so a version of installed Python >= 3.6.0 is required. Use pipenv for installing the required packages in the Pipfile:

$ pipenv --python python3
$ pipenv shell 
$ pipenv install

Running the tests

If you like to see if your installation was successfully, run the tests:

$ pytest .

Usage

Web interface

start web_ui.py

$ python -m beacon.web_ui

start “rest_api.py” in another terminal

$ python -m beacon.rest_api

fill in variant into the fields of the web interface

click submit to see the results of the search

to repeat, click “go Home” button

Command line interface

start “rest_api.py”

$ python -m beacon.rest_api

start “user_cli.py” in another terminal

$ python -m beacon.user_cli

follow instructions on the command line

Maintaining database

To see which flag you can use, call:

$ python3 -m beacon.admin_cli -h 
DB Path:*give "data.db" for maintaining the variant database*
or
DB Path:*give "login.db" for maintaining the user database*

If you want to use a new database or a different one, go to settings.py and change manually the variants PATH_DATABASE and PATH_LOGIN accordingly.

Sphinx documentation

To see the documentation of the source code in HTML-Format, call:

$ open documentation/_build/html/index.html

Authors

  • Namuun
  • Leylanur
  • Julia
  • Leonardo
  • Jin Soo

Contributor who participated in this project Holtgrewe, Manuel.

Acknowledgments

  • We are thankful for the inspiration and continuous help of our supervisor Manuel
  • If you have any concerns or you need help with the software contact him
  • Thank you for using our software :))))

About

FU Berlin Bioinformatik Softwarepraktikum (Projektmanagement) 2020

Resources

Stars

Watchers

Forks

Packages

No packages published