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 Web: http://www.reza-analytics.eu/index.html http://139.59.184.114/index.html
On 1 February 2017 at 19:50, Björn Grüning bjoern.gruening@gmail.com 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
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