forum-index.md

Documentation for Biostars Forum

Here are steps to running and deploying the forum from scratch.

1. Create a virtual environment and clone most recent version of the forum.

2. Install dependencies.

3. Run migrations and tests.

4. Start a local server.

1. Create a virtual environment and clone the repo.

Create a virtual environment by first downloading miniconda at https://docs.conda.io/en/latest/miniconda.html.

After downloading the installation file, run the command ( replace installation_file.sh with your installation file ) :

$ bash installation_file.sh      

Once miniconda has been installed, create a virtual enviroment called engine.

$ conda create -n engine python=3.7

Start the virtual enviorment by entering the command:

$ conda activate engine

Clone or pull the most recent version of the forum by executing:

  git clone https://github.com/ialbert/biostar-central.git  # Clone a new branch
  
  git pull https://github.com/ialbert/biostar-central.git   # Pull into an exisiting 

2. Install dependencies.

Activate the engine virtual enviorment.

$ conda activate engine

Enter the biostar-central directory to install dependencies and requirements into the virtual enviorment.

Execute the following to install python requirements:

pip install -r conf/pip_requirements.txt      # Install python requirements.

Add the following conda channels:

conda config --add channels r
conda config --add channels conda-forge
conda config --add channels bioconda

Execute the following to install all anaconda requirements:

conda install --file conf/conda_requirements.txt  # Install conda requirements.

After dependencies have been installed, a migration needs to be made to create the database collect static files.

3. Run migrations and tests.

Activate the engine virtual enviorment.

conda activate engine

Migrate the forum app by executing the command:

python manage.py migrate --settings biostar.forum.settings

Collect static files for the forum app by executing the command:

python manage.py collectstatic --noinput -v 0 --settings biostar.forum.settings

There is a Makefile command that migrates and collects static files in one shot.

make forum init  # Migrate and collect static files. 

A database has now been created and the static files can be found in biostar-central/export/static/

To ensure installation and migration was successful, run a test by executing the command:

make forum test  # Run tests. 

4. Start a local server

Activate the engine virtual enviorment.

$ conda activate engine

Enter the command make forum serve to start a local server.

make forum serve    # Start local server

The site is now available at http://127.0.0.1:8000/.