Question: Galaxy via Docker?
2
gravatar for vebaev
3.2 years ago by
vebaev130
vebaev130 wrote:

I'm interested using Galaxy via Docker but I have some questions?

-is it only for teaching purposes and after session all data is lost?

-is this mean I can add tools for analysis and regerence genomes, workflows but on next startup all will be lost?

I want to use it for analysing NGS data on my lab server and seems easyer for me than installing local Galaxy and setting it up?

galaxy docker • 1.6k views
ADD COMMENTlink modified 3.2 years ago by Bjoern Gruening5.1k • written 3.2 years ago by vebaev130
5
gravatar for Bjoern Gruening
3.2 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

please have a look at our readme file: https://github.com/bgruening/docker-galaxy-stable

If you mount in a volume Galaxy-Docker will store all information into this mounted volume and your data is stored persistently. This Galaxy-Docker Image is used in production in a few institutions so you should be able to get it running. Please read the documentation and let me know if I can help you in any way!

Cheers,

Bjoern

ADD COMMENTlink written 3.2 years ago by Bjoern Gruening5.1k

Thanks I will read and try, I will notify you if I have difficulties :)

ADD REPLYlink written 3.2 years ago by vebaev130

I have managed to install Docker and run the Galaxy with /export/ option, however I have noticed that after installing some tools my /export/ folder is empty so I realized I run it and made a typo on the name of the export folder - so how to stop the docker and re-run it again with correctly write folder?

Some other minor questions:
-where to put my files on the machine which I want to load in Galaxy for analysis?
-is Docker+ Galaxy are taking lot of memory/CPU, should I leave them running ot stop it when I'm not using it? (my machine have 48 CPU cores and 128GB ram)?
-is there a way to install multiple tools with checkbox from Tool Shed or only one by one?
-if I stop the docker are all tools, genomes, users with all their histories will be saved end when I run it again with /export/ all will be as it is?
-Can I limit the users quota?

Thanks a lot, and sorry for the multiple questions :) 

ADD REPLYlink written 3.2 years ago by vebaev130

- you need to upload files into Galaxy via FTP, via the upload form or via a special folder that needs to be configured in galaxy.ini. Please refere to the general Galaxy wiki here

- I don't think that Docker is using much RAM/CPU and Galaxy is using the a little bit amount to serve the web pages, not much and I don't think it matters much in your setup

- there is currently no way to install multiple tools at once ... but you can use the script shipped with the container: `install-repository`

- Yes if you use /export/ everything will be stored and you can stop your container.

- Sure, you can limit Quota as in every other Galaxy instance

These are all very specific Galaxy question, I highly recommend to read the wiki about Galaxy. The Galaxy Docker project is only deploying Galaxy, you will have all Galaxy goodies and can use all other resources.

Thanks for using Galaxy,

Bjoern

ADD REPLYlink written 3.2 years ago by Bjoern Gruening5.1k
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