biostar-central

by ialbert

Biostar Q&A

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Biostar Central

Software for better science.

Biostar Central is a Python and Django based collection of web applications that support scientific practice and education.

The goal of the project is to produce software with straightforward installation and minimal dependencies that works on any computing platform that supports Python. For each app the philosophy is that of decentralization and self hosting. We write code to allow others to recreate the same services that we run.

Each web application may be deployed individually or in combination with the others. The following applications are currently feature complete:

  • recipes
    a web app that can runs data analysis scripts via a web interface, see: Bioinformatics Recipes
  • forum
    a web app that runs a Q&A forum inspired by StackOverflow, see: Biostars Q&A

Note: The public biostars.org site runs the code from the

biostar2016
branch. The master branch is the development version that we will migrate the main server to in the future.

Installation

The code in Biostar Central requires Python 3.6 or above.

Our installation instructions rely on conda though other alternatives for managing python environments are equally viable.

# Create a virtual environment.
conda create -y --name engine python=3.6

Activate the python environment.

conda activate engine

Clone the source server code and the recipe code.

git clone https://github.com/ialbert/biostar-central.git

Switch to the biostar-engine directory.

cd biostar-central

Install server dependencies.

pip install -r conf/requirements.txt

The installation is now complete.

All server management commands are run through

make
.

Demo server

To run the demonstration version of the

recipes
app execute:
make recipes demo

To run a demonstration version of the

forum
app execute:
make forum demo

Visit http://127.0.0.1:8000/ to view the site.

Default users

All users listed in the

ADMINS
attribute of the Django
settings.py
module will gain administritave privileges when the site is initialized. The
DEFAULT_ADMIN_PASSWORD
attribute will be set as the default admin password. By default the value for both is:
[email protected]

Use this username and password combination to log into the site as an administrator. Change the

DEFAULT_ADMIN_PASSWORD
for public facing installations.

Running the site

The Makefile has several tasks that demonstrate the commands that may be run. Typically a series of

make
tasks may be run. For example

Initialize and run a new

recipes
app.
make recipes serve

Initialize and run a demo version of the recipes app:

make recipes demo

Initialize and run an new

forum
app.
make forum serve

Valid tasks

  • forum
    ,
    recipes
    : selects the app to run. It must be the first task in the list.
  • demo
    : runs a demonstration version
  • init
    : initializes the database schema
  • serve
    : runs the app on the default port (
    localhost:8080
    )
  • save
    : saves the current database content as a JSON fixture file
  • load
    : loads the last database save file from a JSON fixture
  • reset
    : resets the database (deletes all database content)
  • hard_reset
    : runs
    reset
    then deletes all files in the media/spool folder

Testing

To run all tests type:

make test

To test the

recipes
app run:
make recipes test

To test the

forum
app run:
make forum test

Documentation

Additional documentation for:

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