solida-gui

Container Docker application that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow

solida-gui container include:

• solida: Python command-line tool
• Graphical User Interface developed in Django

Requirements

You need docker-engine and docker-compose
See docker-compose docs

For deploying in remote host see ssh-keygen

Quickstart

The first execution could require several minutes, from the second one will be faster.

Using the Makefile

Print the help message

make help

Bring up the solida-gui app

make start

Bring down the solida-gui app

make stop

Manually

Create the workdir tree:

mkdir ~/solida-core             # root path 
mkdir ~/solida-core/config      # path for configuration files
mkdir ~/solida-core/projects    # path where deploying projects in localhost
mkdir ~/solida-core/profiles    # path where storing profiles in localhost
mkdir ~/solida-core/.tmp        # path where storing temporary files
mkdir ~/solida-core/.miniconda  # path where install miniconda
mkdir ~/solida-core/.cache      # Solida cache path

You can change these paths as you prefer, but remember to modify docker-compose.yaml file accordly

...
volumes:
     - ~/solida-core/projects:/home/appuser/projects
     - ~/solida-core/.tmp:/home/appuser/.tmp
     - ~/solida-core/profiles:/home/appuser/.local/share/solida/
     - ~/solida-core/config:/home/appuser/.config/solida
     - ~/solida-core/.miniconda:/home/appuser/miniconda
     - ~/solida-core/.cache:/home/appuser/.cache
...

Clone the repository:

git clone https://github.com/solida-core/solida-gui.git

Cd into the docker directory:

cd solida-gui

Bring up the containers:

docker-compose up

Point your browser to: http://0.0.0.0:8000

Configure and add you pipelines!