JBrowse for SARS-Cov-2 (coronavirus causing covid-19)

This project is used as one of the foundations of http://covbrowser.org/, a pastebin for SARS-CoV-2 genomes. It's a way to get a permanent, shareable URL for a coronavirus isolate, displayed in a genome browser alongside the reference strain, with variants highlighted and annotations that are dynamically updated.

This repo contains the configuration files for a SARS-CoV-2 JBrowse instance with several tracks as well as a Dockerfile for running that instance. A running version of that instance is at

http://covid19.jbrowse.org/

and the Docker image can be obtained from Docker Hub:

https://hub.docker.com/r/gmod/sars-cov-2-jbrowse

Running from Docker

Thanks to Michael Levy (@mglevy) for writing much of the following.

1. Download docker -- this is a useful way to write code so it can run many places and install appropriate dependencies that doesn't mess with code and packages already on the system.

Here's how to do it on ubuntu:

  $ sudo apt-get update
  $ sudo apt-get install docker-engine
  $ sudo service docker start
  $ sudo docker run hello-world

If this works then you get a little print out saying welcome to docker. If not, at the moment, Google is your friend.

For Macs, install Docker from

https://docs.docker.com/docker-for-mac/install/

and Windows:

https://docs.docker.com/docker-for-windows/install/

2. Now type:

  $ sudo docker pull gmod/sars-cov-2-jbrowse
  $ docker run -d -p 8080:80 gmod/sars-cov-2-jbrowse

to download the code and start up your docker instance.

3. Point your web browser to http://localhost:8080/jbrowse/

Building a Docker container yourself

If you would like to build this container yourself, it's pretty easy. After installing Docker, checkout the GitHub repo and run a few docker commands:

  $ git clone https://github.com/GMOD/sars-cov-2-jbrowse.git
  $ cd sars-cov-2-jbrowse
  $ docker build --no-cache -t sars-cov-2-jbrowse -f ./Dockerfile .
  $ docker run -d -p 8080:80 sars-cov-2-jbrowse

and browse to http://localhost:8080/jbrowse. Technically the --no-cache isn't required here but will be necessary for future executions if you want to pull in changes in this repo.

Making changes for yourself or other

That starts to get a little more complicated, but the best way to do that is to fork this repo, make the changes you'd like to make, modify the Dockerfile to pull your forked version and build away. If you'd like to see those change make it back into this repo, feel free to issue a pull request.

Making suggestions or corrections

Please either file an issue at https://github.com/GMOD/sars-cov-2-jbrowse/issues or contact Scott Cain directly at [email protected].