To get the IPD-IMGT/HLA BioSQL Docker image, run this command in your terminal:
$ docker pull nmdpbioinformatics/imgt_biosqldb
You can then run the datbase with the following command in your terminal:
$ docker run -d --name imgt_biosqldb -p 3306:3306 \ -e MYSQL_ROOT_PASSWORD=my-secret-pw nmdpbioinformatics/imgt_biosqldb
If you have a mysql database running locally already, then you can change the first number in the port mapping to something else. If
you change the port then remember to export the
BIOSQLPORT environment variable to whatever you used. A password is required and the
seqann package can access your password if you set the
BIOSQLPASS environment variable.
If you want certain IPD-IMGT/HLA database verions that aren’t loaded into the publicly available docker image, then you can build the image locally with the database versions you want. The sources for IPD-IMGT/HLA BioSQL database can be downloaded from the `Github repo`_.
First clone the public repository:
$ git clone git://github.com/nmdp-bioinformatics/imgt_biosqldb
Then build the docker image and provide the
RELEASES you want to use as an argument.
$ docker build -t imgt_biosqldb:3240-3250 --build-arg RELEASES="3240,3250" .
Once the image has finished building, you can run the database as described above.