Hello Galaxy Team,

We're from the Bioinformatics Shared Resources at Cold Spring Harbor Lab and 
we're trying to create a new flavour of Galaxy for local use in the lab using 
docker containers.

We want to add tools that are specific for our lab, such as importing files 
from our system, onto this flavour of Galaxy using Docker containers. Is there 
a recommended way to do this?

I've taken a look at the README from: 

I have been able to successfully create an instance of Galaxy where the 
homepage is different and tools are imported from the Tool Shed. However, I 
cannot figure out how to install tools onto Galaxy that are not from the Tool 
Shed. I have tried creating a container, putting the tools into the tools 
folder, changing the tool conf and the integrated tool panel xml file. Then 
committing the container and creating a new image. From the new image, I tried 
creating another container and running it. This does not create a Galaxy 
instance with the new tool. (This also does not seem like the best way to go 
about something like this.)

Thank you for your help.

Miuki Yip
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