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Short Description
A proof of concept docker for transmart
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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.

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quartzbio
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