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Last pushed: 10 months ago
Short Description
Mine multiple cancer pharmacogenomic datasets
Full Description

PharmacoDB

PharmacoDB allows scientists to search across publicly available datasets to find instances where a drug or cell line of interest has been profiled, and to view and compare the dose-response data for a specific cell line - drug pair from any of the studies included in the database.

We are providing full access to the contents of PharmacoDB and are distributing the database as a docker image. Making our research fully reproducible is part of the mission of the Haibe-Kains laboratory.

Supported tags

Quick Deployment

Instructions for deploying PharmacoDB are available below:

Note: replace tag with a tag from Supported tags above.

sudo docker pull bhklab/pharmacodb:tag

sudo docker run -d -p 3000:3000 -v ~:/home -it --name pharmacodb --entrypoint /bin/bash bhklab/pharmacodb:tag

sudo docker exec -it --user root pharmacodb /usr/src/app/prod

(The command above will take some time to run, please be patient)

The last command will deploy the web app and it should be accessible on http://localhost:3000. Exiting through Ctrl + C or Ctrl + Z will cause PharmacoDB to shut down. If you want to have further interaction with the docker container please do so in a separate terminal.

MySQL Database Access

In a separate terminal interact with the database by accessing the shell like this:

docker exec -it pharmacodb bash

Once you have accessed the bash shell use the included mysql client to query the database (default password for user root is 'pass'):

mysql -uroot -ppass

or

mysql -u root -p (you will be prompted for password at which point please enter "pass")

PharmacoDB's contents are stored under the pharmacodb_development database which can be accessed using standard SQL.

USE pharmacodb_development;
SHOW TABLES;

Create PostgreSQL Database Dump

In a separate terminal run the following command:

sudo docker exec -it --user root pharmacodb /usr/src/app/data/mysql_to_postgres

The dump should be available in your home directory: ~/pharmacodb_development.psql

Note

All the data in the bhklab/pharmacodb:1.1.1 Docker image corresponds to the following Zenodo dataset: 10.5281/zenodo.1143644

For more information, please visit https://pharmacodb.pmgenomics.ca

Docker Pull Command
Owner
bhklab