Hello Bjoern,

Thanks for the quick response, I appreciate that.

Concerning the instructions, I am unclear of a couple of things.

I have a folder with my tools, there is no preinstalled folder that these tools 
need to go in called my_tools_folder, right? Additionally, would I place this 
tool in the same directory level as Galaxy_Central or as the config directory?
(My current set up is galaxy_storage -> galaxy-central -> config, I have my 
tools folder in the same level as galaxy-central.)
 
Lastly, the environment variable, is there a specific file that all the 
environment variables are stored for docker Galaxy? I have tried looking for an 
env file, but could not find it.

Thanks so much!
Miuki
________________________________________
From: Björn Grüning [bjoern.gruen...@gmail.com]
Sent: Wednesday, July 20, 2016 2:23 AM
To: Yip, Miu ki; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not 
in Toolshed

Hi Miuki!

Am 19.07.2016 um 22:36 schrieb Yip, Miu ki:
> 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?

Can you try the following, assuming that all your tools are in
my_tools_tolder.

ADD ./my_tools_folder /inhouse_tools/

Now we need a tool_conf.xml file. You can create an additional one, no
need to modify the existing one. I would propose to include this config
file also in ./my_tools_folder so it will end up in
/inhouse_tools/tool_conf.xml
With the following environment variable you tell Galaxy about the
additional tool_conf file.

ENV GALAXY_CONFIG_TOOL_CONFIG_FILE =
config/tool_conf.xml,config/shed_tool_conf.xml,/inhouse_tools/tool_conf.xml

Please make sure that your new tools in /inhouse_tools/tool_conf.xml
have as path "/inhouse_tools/XXXX.xml".

Let me know if this works, we should add this to the readme.

Thanks,
Bjoern

> I've taken a look at the README from:
> https://github.com/bgruening/docker-galaxy-stable
>
> 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.
>
> Best, Miuki Yip
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