This tutorial explains how to install and run a BridgeDb Identifier Mapping Service (IMS) with gene-to-variant and variant-to-gene functionality.
Download the linksets data you want to load into the IMS from http://bridgedb.org/data/gene_database/linkset/.
A prerequisite is a Docker installation. You can download Docker from various places and many GNU/Linux distributions ship a version as part of their distribution. Other options include:
Pull the IMS docker image:
docker pull openphacts/identitymappingservice
Create the mysql docker image to store the linksets:
docker run --name mysql-for-ims -e MYSQL_ALLOW_EMPTY_PASSWORD=yes \ -e MYSQL_DATABASE=ims -e MYSQL_USER=ims -e MYSQL_PASSWORD=ims \ -d mysql
The next command line example assumes that the file
load.xml is present the
docker run --link mysql-for-ims:mysql -v /home/johndoe/data5:/staging \ openphacts/identitymappingservice loader file:///staging/load.xml
MINGW64 / Windows:
docker run --link mysql-for-ims:mysql -v /c/Users/johndoe/data5:/staging openphacts/identitymappingservice loader file:///staging/load.xml
An example of the load.xml file (more info):
<?xml version="1.0"?> <loadSteps> <clearAll/> <void>file://staging/Ensembl_SNP_dataset.void.ttl</void> <linkset>file:///staging/PolyPhen_91.ttl</linkset> </loadSteps>
docker run --name ims --link mysql-for-ims:mysql -p 8081:8080 -d openphacts/identitymappingservice
You can confirm the instance is running with:
Both these commands will give you a long identifier which you should remember for later.
Open the following webpage in a browser:
It should look like this:
Shutting down the docker is done with the command docker stop and the identifier you got with the docker run or docker ps commands, for example:
docker stop b5e9715818f6
docker stop ims
ims happens to be the ID/name for the running image for the author at the time of writing.
You can delete the images with:
docker container rm b5e9715818f6 d989788c0b03
Where the two IDs are the one for the MySQL-IMS docker and the IMS docker containers.