docker-galaxy image with custom tools as new container?
Dear Galaxy-Devs, I am currently developing a tool/workflow based on KNIME platform for data analysis. The plan is for my group to publish this tool at some point and we decided that Galaxy might be a very good platform to base it on. Galaxy could simply run KNIME on a server (along with R script inside the KNIME workflow) and serve the output files to the user. However, I am quite new to the Docker concept and I am not sure if I get it right. Do you think I could take the Galaxy Docker image ( https://github.com/bgruening/docker-galaxy-stable) and edit the container so it would also contain KNIME and R with our workflow ? This way I would like to obtain a Docker container that would have both this Galaxy version plus our tools and that could be simply moved to another machine to show, say, to my boss or deploy on a server for testing ?
From the webpage I got the feeling that those docker images an non-editable, is that right ?
I would be very thankful for helping me with the first steps! All the best, Piotr
Hi Piotr, Am 04.09.2015 um 17:58 schrieb Piotr Grabowski:
Dear Galaxy-Devs,
I am currently developing a tool/workflow based on KNIME platform for data analysis. The plan is for my group to publish this tool at some point and we decided that Galaxy might be a very good platform to base it on. Galaxy could simply run KNIME on a server (along with R script inside the KNIME workflow) and serve the output files to the user.
You mean headless KNIME?
However, I am quite new to the Docker concept and I am not sure if I get it right. Do you think I could take the Galaxy Docker image ( https://github.com/bgruening/docker-galaxy-stable) and edit the container so it would also contain KNIME and R with our workflow ?
Yes this is possible. You can build on top of this Image and add your additional packages. Indeed we do this a lot. We call it Galaxy flavours. You simply add all the tools you want to have and get a full-featured Galaxy instance for your users. For example see our GalaxyP flavour: https://github.com/bgruening/docker-galaxyp
This way I would like to obtain a Docker container that would have both this Galaxy version plus our tools and that could be simply moved to another machine to show, say, to my boss or deploy on a server for testing ?
Sure, we do this exactly this way.
From the webpage I got the feeling that those docker images an non-editable, is that right ?
A Docker Image is non-editable, but you can create a new one on top of it and (as integrated in galaxy-stable) we export all configuration files, user files etc. to the host, so everything is saved outside of the container.
I would be very thankful for helping me with the first steps!
Does this answer help? Out of curiosity wouldn’t it be simpler to plug your tools into Galaxy directly than using such a bridge between Galaxy and KNIME? Cheers, Bjoern
All the best, Piotr
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
-
Björn Grüning -
Piotr Grabowski