Tripal, Docker, Galaxy

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Tripal, Docker, Galaxy

Anthony Bretaudeau-2
Hi all,

Some developments have occurred lately around Tripal, Docker and Galaxy,
so I think it's time to write a little email to keep everyone informed
on what is going on.

For those of you who were at the GMOD meeting in Bloomington, this is a
follow-up to the things Eric Rasche presented, in particular the "galaxy
genome annotation" project: https://github.com/galaxy-genome-annotation

Briefly, the goal is to integrate GMOD tools (including Galaxy) into a
docker based infrastructure, and to make them work together as much as
possible. The development on this project is occurring there:
https://github.com/galaxy-genome-annotation/dockerized-gmod-deployment


Concerning Tripal specifically, here are the news:

- There is now an up-to-date (=2.x-dev) Tripal Docker image available,
development and documentation is there:
https://github.com/erasche/docker-tripal

- To build it, there is now a Chado 1.31 database dump available. There
are 3 flavors (raw chado ; chado + ontologies ; chado + ontologies +
tripal specific changes) there:
https://cpt.tamu.edu/jenkins/job/Chado-Prebuilt-Schemas/ and the project
is on github too: https://github.com/erasche/chado-schema-builder

- There is also a python module that allows to load data into a Tripal
instance from command line (or python code):
https://github.com/abretaud/python-tripal

- This python-tripal module uses the drupal module tripal_rest_api,
available there: https://github.com/abretaud/tripal_rest_api

- If you love python, you can also interact directly with a Chado db
using another (still very incomplete) python module:
https://github.com/abretaud/python-chado

The goal is (one day) to have galaxy tools able to use these python
modules to load data into Tripal or a Chado db directly.

For the moment it should already be easy to write a simple bash script
to deploy a tripal instance and load a complete dataset into it
automatically (for example the test data from the tutorial).
(personnally I found it very useful for tests and reproducibility).


All of this is still young and needs a lot of testing and debugging, if
you are interested, don't hesitate to contribute!

Specifically:

- we just managed to generate the 1.31 Chado dump and to migrate from
tripal 2.0 to 2.x-dev, so we haven't yet tested if everything is ok. Any
help on testing it would be very much appreciated :)

- we added some default tripal modules to the docker image, if you think
other ones deserve to be included, just get in touch!


That's it for today.


Thanks for reading!

Anthony Bretaudeau


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