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How to include local tools with Docker image of Galaxy ?

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How to include local tools with Docker image of Galaxy ?

Md. Rezaul Karim
Dear All,

I'm a new user of Galaxy. I have been exploring the things and trying to use the Docker image of Galaxy. Eventually, I am planning to run the docker container on our local Cluster.

I was wondering if there's any way to include local tools with the Dockerfile. For example using the Docker image of Galaxy at https://github.com/bgruening/docker-galaxy-stable it shows how to include the tools to the Docker image of Galaxy from the Galaxy tool shed as follows:

RUN install-repository \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7" \
    "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_pdf_api2_2_023" \

This command will pull the tools from the Galaxy tool shed and install inside the docker container. But, is there's any similar way to include my own local tools?




Regards,
_________________________________
Md. Rezaul Karim, BSc, MSc
PhD Researcher, INSIGHT Centre for Data Analytics
National University of Ireland, Galway
IDA Business Park, Dangan, Galway, Ireland

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Re: How to include local tools with Docker image of Galaxy ?

Björn Grüning-3
Hi,

sure this is possible! :)
We have some small documentation about this here:

https://github.com/bgruening/docker-galaxy-stable/#integrating-non-tool-shed-tools-into-the-container--toc

Cheers,
Bjoern

Am 01.02.2017 um 16:31 schrieb Md. Rezaul Karim:

> Dear All,
>
> I'm a new user of Galaxy. I have been exploring the things and trying to
> use the Docker image of Galaxy. Eventually, I am planning to run the
> docker container on our local Cluster.
>
> I was wondering if there's any way to include local tools with the
> Dockerfile. For example using the Docker image of Galaxy at
> https://github.com/bgruening/docker-galaxy-stable it shows how to
> include the tools to the Docker image of Galaxy from the Galaxy tool
> shed as follows:
>
> RUN install-repository \
>     "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_numpy_1_7" \
>     "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_perl_pdf_api2_2_023" \
>
> This command will pull the tools from the Galaxy tool shed and install
> inside the docker container. But, is there's any similar way to include
> my own local tools?
>
>
>
>
> Regards,
> _________________________________
> *Md. Rezaul Karim*, BSc, MSc
> PhD Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
> <http://139.59.184.114/index.html>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: How to include local tools with Docker image of Galaxy ?

Md. Rezaul Karim
Hi Bjorn,

Thank you very much for your answer. I followed the instruction from the page you mentioned and trying to add some of my own tools (i.e. non-shed tools) to Docker image of Galaxy. I used the following command:

sudo docker run -d -p 8080:80 -p 8021:21 -p 8022:22 -v /home/asif/local_tools/:/local_tools -e "GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml.sample,/local_tools/my_tools_conf.xml" my_galaxy:1902

Here:
1. -v /home/asif/local_tools/:/local_tools is used to mount the local tool directory
2. -e "GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml.sample,/local_tools/my_tools_conf.xml" is used to show local tool path
3. my_galaxy:1902 is the Galaxy image with TAG that I prepared from bgruening/galaxy-stable:dev

The docker instance starts successfully. However, when accessing the server on http://localhost:8080/, I only see the built-in tools means I don't see the name of my tools.


I also tried running the docker image in an interactive mode using the following command:
sudo docker run -i -t -p 8080:80 -p 8021:21 -p 8022:22 -v /home/asif/local_tools/:/local_tools -e "GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml.sample,config/shed_tool_conf.xml.sample,/local_tools/my_tools_conf.xml" my_galaxy:1902

But I am getting following errors: galaxy:galaxy_nodejs_proxy: ERROR (abnormal termination)

Please note that the location of the configuration file for my local tools is: /home/asif/local_tools/my_tools_conf.xml, and the location of the tools is:
/home/asif/my_tools/

The log also says that the Galaxy server is serving on http://127.0.0.1:9001
However, when I try to access this on my browser, it doe's not show anything but "Unable to connect".


Please help.





Regards,
_________________________________
Md. Rezaul Karim, BSc, MSc
PhD Researcher, INSIGHT Centre for Data Analytics
National University of Ireland, Galway
IDA Business Park, Dangan, Galway, Ireland

On 1 February 2017 at 19:50, Björn Grüning <[hidden email]> wrote:
Hi,

sure this is possible! :)
We have some small documentation about this here:

https://github.com/bgruening/docker-galaxy-stable/#integrating-non-tool-shed-tools-into-the-container--toc

Cheers,
Bjoern

Am 01.02.2017 um 16:31 schrieb Md. Rezaul Karim:
> Dear All,
>
> I'm a new user of Galaxy. I have been exploring the things and trying to
> use the Docker image of Galaxy. Eventually, I am planning to run the
> docker container on our local Cluster.
>
> I was wondering if there's any way to include local tools with the
> Dockerfile. For example using the Docker image of Galaxy at
> https://github.com/bgruening/docker-galaxy-stable it shows how to
> include the tools to the Docker image of Galaxy from the Galaxy tool
> shed as follows:
>
> RUN install-repository \
>     "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_numpy_1_7" \
>     "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_perl_pdf_api2_2_023" \
>
> This command will pull the tools from the Galaxy tool shed and install
> inside the docker container. But, is there's any similar way to include
> my own local tools?
>
>
>
>
> Regards,
> ______________________________
___
> *Md. Rezaul Karim*, BSc, MSc
> PhD Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
> <http://139.59.184.114/index.html>
>
>
> ______________________________
_____________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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