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!
From: Björn Grüning [bjoern.gruening(a)gmail.com]
Sent: Wednesday, July 20, 2016 2:23 AM
To: Yip, Miu ki; galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed
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
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
With the following environment variable you tell Galaxy about the
additional tool_conf file.
ENV GALAXY_CONFIG_TOOL_CONFIG_FILE =
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.
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.
Best, Miuki Yip
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