search

bgruening / docker-galaxy

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy
MIT License
226 stars 134 forks source link

Adding custom tools for galaxy docker instance #461

Closed mohan-XD closed 5 years ago

mohan-XD commented 6 years ago

I'm trying to add a tool from the test toolshed. since it is not avilable through the galaxy interface, I downloaded it and then tried to add as custom tools to the galaxy docker instance but it doesn't work.

This is the code:

docker run -it --mount type=bind,source="$(pwd)",target=/local_tools --env "GALAXY_CONFIG_TOOL_CONFIG_FILE =config/tool_conf.xml.sample,config/shed_tool_conf.xml.sample,local_tools/my_tools_conf.xml" -p 8080:80 -p 8021:21 -p 8022:22 bgruening/galaxy-stable

working directory : galaxy/tools/local_tools

inside local_tools i have : filtering.py filtering.xml my_tools_conf.xml

This error comes up over and over :

DEBUG:galaxy.app:python path is: lib/, lib/, ., , /galaxy_venv/bin, /galaxy_venv/lib/python2.7, /galaxy_venv/lib/python2.7/plat-x86_64-linux-gnu, /galaxy_venv/lib/python2.7/lib-tk, /galaxy_venv/lib/python2.7/lib-old, /galaxy_venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /galaxy_venv/local/lib/python2.7/site-packages DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 65, in init self.config.check() File "lib/galaxy/config.py", line 827, in check raise ConfigurationError("Tool config file not found: %s" % path) ConfigurationError: Tool config file not found: ./local_tools/my_tools_conf.xml

can somebody tell me what would be wrong with this procedure?

bgruening commented 6 years ago

You can enable test toolshed installation with -e ENABLE_TTS_INSTALL=True see here for more information: https://github.com/bgruening/docker-galaxy-stable#magic-environment-variables--toc

Otherwise, I think you need to specify an absolute path in your path to the shed_tools file: "GALAXY_CONFIG_TOOL_CONFIG_FILE =config/tool_conf.xml.sample,config/shed_tool_conf.xml.sample,/local_tools/my_tools_conf.xml"

mohan-XD commented 6 years ago

Thank you. Sorry for the late reply. The 1st method worked well and I got the test toolshed on the interface. thank you again.

bgruening commented 6 years ago

Awesome, thanks for reporting back!