quartzbio/transmart repository overview

⁠transmart-docker

A proof of concept docker for transmart

⁠Disclaimer

This work is only a proof of concept, and should only be used for testing purposes. It is not distributed by the Transmart foundation nor by the eTRIKS consortium.

⁠What is it ?

This docker provides a fat container running tomcat, solr, Rserve and Postgres, to deliver the transmart web-app.

⁠transmart version

The transmart software currently provided in the master branch is transmart.war.1.2.2.e.fg-fix as downloaded from https://portal.etriks.org/Portal/⁠

⁠How to use it ?

clone the repository, and type: make run By default it will bind the docker ports to your computer, then point your browser to: http://localhost:8080/transmart⁠

N.B: If you use boot2docker (e.g. on MacOsX or Windows), use instead the boot2docker ip (e.g. http://192.168.59.103:8080⁠).

⁠how to connect to the Postgres instance running inside the docker

The ports should be forwarded, so that you should be able to connect from your computer:

PGPASSWORD=biomart_user psql transmart -h localhost -U biomart_user

⁠actual deployment

in a real-life deployment, a lot of files should actually be written on the host or in a data volume:

• the database files (currently in /var/lib/postgresql/tablespaces)
• the logs: in /var/logs/ and /var/log/supervisor/
• the data files (CEL files): ?

⁠Implementation

I used the installation instructions from here: https://wiki.transmartfoundation.org/pages/viewpage.action?pageId=6619205⁠

⁠postgres

To be able to connect from the host computer, I had to mess with postgresql.conf and pg_hba.conf in /etc/postgresql/9.3/main/.

⁠solr port

We had to set the solr port in /usr/share/tomcat7/.grails/transmartConfig/Config.groovy

⁠supervisor: for running services

In a docker, quite often we can not use the normal startup scripts. I used supervisor as a simple way to start the required services, have a look at supervisord.conf to check it.

⁠Troubleshooting, TODO

⁠Sample Details not working

I get an endless "Loading" message.

⁠pdi-ce-4.4.0-stable.tar.gz quite huge

the transmart-data could probably try to avoid this big download.

⁠split the docker into many sub-dockers

Instead of a big monolithic container, we could use one for the database, one for solR, one for solR.

⁠reduce the overall size

It is currently probably overweighted.