sanjayboddu/ensweb-website repository overview

⁠Ensembl website docker

⁠Pre-requisites

Docker (https://www.docker.com/get-docker⁠)

A local mysql instance serving an Ensembl sessions database is required - this must be accessible from your docker container. You'll need to set up a local mysql server, then create a user and database as follows.

Create the ensrw user and grant required priviledges

mysql> CREATE USER 'ensrw'@'%' IDENTIFIED BY 'ensrw';
mysql> GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, REFERENCES, INDEX, ALTER, CREATE TEMPORARY TABLES, LOCK TABLES ON `%`.* TO 'ensrw'@'%';

Create the ensembl_session database

mysql> CREATE DATABASE `ensembl_session`

Now create the table schema using the SQL file here http://ftp.ensembl.org/pub/release-90/mysql/ensembl_accounts/⁠

⁠Build and run

⁠Build the image

git clone https://github.com/nicklangridge/webdocker-website
cd webdocker-website

docker build --rm --no-cache --build-arg ENSEMBL_SERVERNAME=my-ensembl --build-arg SESSION_HOST=my-local-mysql --build-arg SESSION_PORT=3306 --build-arg SESSION_USER=ensrw --build-arg SESSION_PASS=ensrw -t webdocker-website:latest .

Some arguments must be specified at build time:

• ENSEMBL_SERVERNAME - (required) this is the domain name of your Ensembl server - if you are not using a domain name you should set this to the external IP of your docker container
• SESSION_HOST - (required) host name of the mysql instance serving the sessions db
• SESSION_PORT - (default=3306) port number of the mysql instance serving the sessions db
• SESSION_USER - (default=ensrw) sessions db user name
• SESSION_PASS - (default=ensrw) sessions db user password

⁠Run a container

Run a container in daemon mode

docker run -p 80:8080 -dt webdocker-website:latest

The website should now be available on port 80.

For debugging you may want to run a container in interactive mode

docker run -p 80:8080 -it webdocker-website:latest bash

Now you can explore the running container from the command line.