bioedge/edge-covid19 repository overview

⁠Requirements

• Docker Engine version 19.03.2 or greater
• Recommended minimum computational resource: 8 GB memory. 4 CPUs. 20GB storage space for the image

⁠How to install this image? A step by step guide:

⁠Step 1: Install and run Docker

This step can be skipped if you have docker installed and opened in your system. If a docker instance is running in a MacOSX, dockers’s icon () will show up at the top bar of your screen.

If you do not have docker installed, See https://www.docker.com/products/docker-desktop⁠ to download and install a copy.

⁠Step 2: Obtain the docker image

The image size is around 12.3GB. On a MacOSX, open Terminal and cd into the directory where you want to install the image. If you want to create a new folder, then first create that folder, and then pull the docker image:

$ mkdir EDGE-COVID19

$ cd EDGE-COVID19

$ docker pull bioedge/edge-covid19

This can take anywhere from 10-30 minutes depending on your internet speed.

⁠Step 3: Setup necessary databases and folders

Pull MySQL database for User Management and create a volume

$ docker pull bioedge/edge_ubuntu_mysql

$ docker create --name mysql_data --volume /var/lib/mysql  bioedge/edge_ubuntu_mysql

Create Output and Report directories

$ mkdir -p EDGE_output  EDGE_report  EDGE_input/public/data

Download human GRCh38 genome⁠ for host removal.

$ wget https://ref-db.edgebioinformatics.org/EDGE/ncov/human_ref_GRCh38_all.fa.gz⁠

⁠Step 4: Start EDGE COVID-19 instance

Start the EDGE COVID-19 by running the following command in your Terminal from the EDGE-COVID19 folder.

$ docker run -d --volumes-from mysql_data  \

-v $PWD/EDGE_output:/home/edge/EDGE_output \

-v $PWD/EDGE_input:/home/edge/EDGE_input \

-v $PWD/EDGE_report:/home/edge/EDGE_report \

-v $PWD/human_ref_GRCh38_all.fa.gz:/home/edge/edge/database/human_ref_GRCh38_all.fa.gz \

-p 80:80 -p 8080:8080 --name edge_ncov bioedge/edge-covid19

Wait a few minutes for the docker image to start the EDGE service; then open http://localhost/⁠ in a browser (Firefox, Chrome, Safari) to start the EDGE COVID-19. The instance will keep running. You will see the following screen:

⁠Step 5: Login information

If EDGE COVID-19 is to be used by a single user then there is no need to create an account. You can log in directly using following credentials by clicking on the Login button on top right:

EDGE user: [email protected]

EDGE password: admin_docker

⁠Tutorial & Help

• The detailed user guide can be found here⁠.
• The EDGE tutorial video series for original EDGE platform hosted in Youtube⁠.

⁠Contact:

You can view the discussions in the google group below and join the group to post questions or comments.

EDGE user’s google group at https://groups.google.com/d/forum/edge-users⁠ or contact us at [email protected]⁠.

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