I apologize for all the questions, but would all of this work be done within the container
after it is created by the Docker run command or are you referring to the local out of
I am getting an error like:
DEBUG:galaxy.app:python path is: lib/, ., ,
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 63, in paste_app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
File "lib/galaxy/app.py", line 44, in __init__
File "lib/galaxy/config.py", line 636, in check
raise ConfigurationError("Tool config file not found: %s" % path )
ConfigurationError: Tool config file not found:
if I try to run when I am adding outside of the container, I've cat-ed the path and
standard out displays the contents of the file. I am getting another error about files not
being found also when I add to the container itself when I attach.
Thanks so much,
From: Björn Grüning [bjoern.gruening(a)gmail.com]
Sent: Wednesday, July 20, 2016 2:05 PM
To: Yip, Miu ki; Björn Grüning; galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed
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?
No, you can create such a folder wherever you want and name it like you
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.)
This does not matter, what matters is that the folder path is correct in
the env variable.
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.
There is no file. These are real environment variables that are created
by Docker during container start. You can change them during start with
(e.g): docker run -e MY_ENV_VAR=foo bgruening/galaxy-stable
If such a variable, beginning with GALAXY_CONFIG_XXX exists this will be
picked up by Galaxy. Have a look at the container there are a lot
GALAXY_CONFIG_ vars set.
Hope this helps,
Thanks so much! Miuki ________________________________________ 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
/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 =
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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