cBioPortal/cbioportal-docker

Name: cbioportal-docker

Owner: cBioPortal

Description: Context to create cBioPortal docker images

Forked from: thehyve/cbioportal-docker

Created: 2016-12-14 17:03:32.0

Updated: 2016-09-14 17:13:39.0

Pushed: 2017-12-07 16:08:57.0

Homepage: null

Size: 36

Language: null

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README

cbioportal-docker

Download and install Docker from www.docker.com.

Notes for non-Linux systems

Step 1 - Setup network

Create a network in order for the cBioPortal container and mysql database to communicate.

er network create cbio-net

Step 2 - Run mysql with seed database

Download the seed database from datahub seedDB space

This command imports the seed database file into a database stored in /<path_to_save_mysql_db>/db_files/ (:warning: this should be an absolute path in command below), before starting the MySQL server.

:warning: This process takes about 45 minutes. For much faster loading, we can choose to not load the PDB data, by removing the line that loads cbioportal-seed_only-pdb.sql.gz. Please note that your instance will be missing the 3D structures view feature (in mutation view) if you chose to leave this out.

er run -d --name "cbioDB" \
restart=always \
net=cbio-net \
 8306:3306 \
 MYSQL_ROOT_PASSWORD=P@ssword1 \
 MYSQL_USER=cbio \
 MYSQL_PASSWORD=P@ssword1 \
 MYSQL_DATABASE=cbioportal \
 /<path_to_save_mysql_db>/db_files/:/var/lib/mysql/ \
 /<path_to_seed_database>/cgds.sql:/docker-entrypoint-initdb.d/cgds.sql:ro \
 /<path_to_seed_database>/seed-cbioportal_no-pdb_hg19.sql.gz:/docker-entrypoint-initdb.d/seed_part1.sql.gz:ro \
 /<path_to_seed_database>/seed-cbioportal_only-pdb.sql.gz:/docker-entrypoint-initdb.d/seed_part2.sql.gz:ro \
sql

:warning: Please follow the logs of this step to ensure no ERRORs occur. You can follow the logs by running:

 docker logs -f cbioDB

If any ERROR occurs, make sure to check this. A common problem is getting an ERROR by pointing the -v parameters above to files/folders that do not exist.

Step 3 - Build the Docker image containing cBioPortal

Checkout the repository, enter the directory and run build the image.

clone https://github.com/thehyve/cbioportal-docker.git
bioportal-docker
er build -t cbioportal-image .

Alternatively, if you do not wish to change anything in the Dockerfile or the properties, you can run:

er build -t cbioportal-image https://github.com/thehyve/cbioportal-docker.git

Step 4 - Run the cBioPortal container

er run -d --name="cbioportal-container" \
restart=always \
net=cbio-net \
 8081:8080 \
ioportal-image

cBioPortal can now be reached at http://localhost:8081/cbioportal/

Activity of Docker containers can be seen with:

er ps -a

Uninstalling cBioPortal

First we stop the Docker containers.

er stop cbioDB
er stop cbioportal-container

Then we remove the Docker containers.

er rm cbioDB
er rm cbioportal-container

Cached Docker images can be seen with:

er images

Finally we remove the cached Docker images.

er rmi mysql
er rmi cbioportal-image

Data Loading & More commands

For more uses of the cBioPortal image, see example_commands.md