SOM-Browser

This repository contains a complete copy of the Boyle Lab Human-Mouse SOM Browser, described in Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. Diehl AG, Boyle AP. Nucleic Acids Research 2018, :gky018.

The SOM Browser runs on two linked Docker containers: one containing the Catalyst web app and nginx web server and the second containing the mySQL database. To set up a local mirror, follow the directions under "INSTALLATION"

INSTALLATION

To streamline the installation process, we have provided the "install_browser.sh" script, which automates all the steps to initialize the Docker containers. Before running this, you will need to make some minor edits to it and some other files in the SOM-Browser directory:

1. (Optional) Set the "BROWSER_PATH" variable at the head of "install_browser.sh" to the absolute path where the browser files exist. This defaults to the MouseSOM subdirectory of the present working directory.

2. Edit the "server name" variable in "nginx.conf" to match the name and port number of the host machine.

3. (Optional) Enable browser monitoring on the docker container by uncommenting the relevant sections in install_browser.sh and editing the marked sections in monitrc to match your email server and email address.

4. Run the install_browser.sh script:

   ./install_browser.sh

5. (Optional, but highly recommended!) Log in to the db container with the command:

   docker exec -it db bash

   then log in to mysql, as root, with password "CHANGE_ME" and change the password following normal procedures.

STARTING AND STOPPING THE BROWSER

Shell scripts are provided to easily start and stop the browser:

./start_browser.sh ./stop_browser.sh

If you installed with monit enabled, you may also start the browser using the following command. (This will also enable monitoring of an already-running browser instance.)

./monit_browser.sh

UNINSTALLING THE BROWSER

To completely remove the browser, issues the following two commands after stopping the browser with stop_browser.sh:

docker rm -v db MouseSOM

If desired, you can now delete the entire MouseSOM directory and its contents.

GETTING HELP / BUG REPORTS

Please submit pull requests through GitHub. Bug reports and questions can be emailed to adadiehl@umich.edu.