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?
I asked for help at the dedicated Gitter channel: https://gitter.im/bgruening/docker-galaxy-stable?at=5bdcb3cbcd2a6b5bdc8761de
They may post back here, or at the chat, and please feel free to join in the conversation there. Something looks to be wrong with the paths in the install command but I'm sure not exactly how to fix it, if there are known issues, etc.
Thanks! Jen, Galaxy team
Cross-posted here: https://github.com/bgruening/docker-galaxy-stable/issues/461