News: Galaxy Docker Image (v 15.03)
2
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi all!

We are proud to present you the next release of Galaxy Docker.

https://github.com/bgruening/docker-galaxy-stable
https://registry.hub.docker.com/u/bgruening/galaxy-stable/

A few highlights:

* based on Galaxy 15.03, with all it's new awesome features
* Docker image is now based on Ubuntu 14.04
* move all required Galaxy dependencies to toolshed/requirements
* use Ansible roles to build large parts of the image
* export the supervisord web-interface (port 9002)
* enable Galaxy reports webapp on GALAXY_URL/reports
* enable/disable services like FTP or Galaxy reports during start-up

The IPython integration was also updated and has a few new libraries to make it more convenient for R users.

A big thanks to John Chilton for his enormous support and constant input.

The following new releases are available:

 * docker pull bgruening/galaxy-stable:latest_2015.01.13
 * docker pull bgruening/galaxy-stable:15.03
 * docker pull bgruening/galaxy-stable (-> currently 15.03)

As usual feedback is more than welcome!

Cheers,
Bjoern

release docker galaxy news ipython • 1.5k views
ADD COMMENTlink written 3.5 years ago by Bjoern Gruening5.1k

HI Bjoern

I know this is a very naive question but what are the advantages  and disadvantages (particularly for newbies like me) of using a docker installation (ignoring for  teaching purpose). 

I can see that on the second of the links you give above it states 'The GalaxyDocker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features.

Why don´t you recommend your  docker installation be used for a normal installation intend for normal data analysis.

Thanks  Guy 

ADD REPLYlink written 3.5 years ago by Guy Reeves1.0k
1

Hi Guy,

we have plans to make deployment, especially migration of different versions easier. Moreover, docker has some security implications you need to be aware of. You can work around them, but it leaves a bad taste if I would recommend it for production.

That said, I know that the Max Planck Institute of Immunobiology and Epigenetics is using this Docker Image in production and there are some institutions that are evaluating this concept currently, also for sensible data. Maybe I'm just to cautious and there are many more users that are using it already in production.

Is this answering your question?

Ciao,

Bjoern

 

ADD REPLYlink written 3.5 years ago by Bjoern Gruening5.1k

HI Bjoren

Thanks for the answer it is very useful but I do have a few other questions, if you have time.

As far as I understand the big advantage is that for newbies installation is very much easier .It also has the potential to extend Galaxy installations to PCs and Macs, which could be very useful if people want their own personal Galaxy installation.

But I am a little unclear about what you get after a successful docker installation of Galaxy.

1    Are a suite of tools installed similar to usegalaxy.org? —personally it was installing Picard tools which I ultimately failed with when trying to set up my own congenital installation, I had everything else sorted including FTP, accounts enabled ….

2    Is an FTP capacity  already enabled (including specifying the upload folder)?

3     Is the capacity to register accounts enabled (including administrators) ?

4    In terms of performance (processing speed of tools ) does using the the docker installation have a significant cost ?

5    How is updating handled, just the same as a normal installations?

You mention security concerns, could you briefly elaborate.  If the server was only accessed within a secure network would this remove these issue(s)?

Thanks  Guy

ADD REPLYlink written 3.5 years ago by Guy Reeves1.0k

Hi Guy,

you are correct, you can run this Image on every platform Docker can be installed.

> 1    Are a suite of tools installed similar to usegalaxy.org? —personally it was installing Picard tools which I ultimately failed with when trying to set up my own congenital installation, I had everything else sorted including FTP, accounts enabled ….

The bgruening/galaxy-stable contains the standard Galaxy Installation. As more and more tools are migrated out of Galaxy to the Tool Shed this image will have less pre-installed tools over time. Nevertheless, we offer you special images with a set of predefined tools, for example bgruening/galaxy-deeptools, bgruening/galaxy-rna-workbench, bgruening/galaxy-chemicaltoolbox. It's really easy to create such Galaxy flavours and if you provide me a list of tools I can create you one.

> 2    Is an FTP capacity  already enabled (including specifying the upload folder)?

Yes, it's integrated by default.

> 3     Is the capacity to register accounts enabled (including administrators) ?

You have an admin account from the beginning. You should deactivate this account in a production instance or change the password. With this account you can create new users, install tools etc. You can also change every setting from `config/galaxy.ini` during container start, via environment variables. In the end you can change every single detail that you can change with a normal installation also with this container.

> 4    In terms of performance (processing speed of tools ) does using the docker installation have a significant cost?

Short: No.

Long: Depends a little bit on your operating system. Under OS-X and Windows you need to have a VM (boot2docker). This VM can take a little bit of memory and has a overall overhead.

> 5    How is updating handled, just the same as a normal installations?

Just the same. You will not see a difference.

Hope this helps,

Bjoern

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Bjoern Gruening5.1k

HI Bjoren

 

​Thanks a lot for the answers and your kind offer to make up a Galaxy Flavour. Am I correct in saying that you do not list the tools already included in the the Galaxy Flavours linked to above ? (if you do I cannot find them).

 I will sit down soon and make a list of all the tools I use and and get back to you.

Thanks  Guy

 

ADD REPLYlink written 3.5 years ago by Guy Reeves1.0k

Yes you are correct, I haven't listed them in the readme file. Nevertheless, if you click on the Dockerfile tab, you can maybe guess all tools. Search for something like --name deeptools this name is in most cases the tool name.

ADD REPLYlink written 3.5 years ago by Bjoern Gruening5.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 94 users visited in the last hour