Local galaxy file not found

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1

Hi everyone,
I’m trying to use galaxy in local using docker on a virtual machine but I’m having some problems with the configuration.
In the home I have the galaxy folder organised as follow:

-galaxy:
–docker.sh
–config:
—tool_conf.xml
—tools_sheds_conf.xml
–tools:
—get_pheno.py (the tool I’m creating)
—get_pheno.xml

And the docker.sh file is a bash script containing the following code:

#!/usr/bin/env bash

docker run -i -t \
    -p 8080:80 -p 8021:21 -p 9002:9002 \
    --privileged=true \
    -e "NONUSE=reports" \
    -e "GALAXY_CONFIG_ADMIN_USERS=(my-mail)" \
    -e "GALAXY_CONFIG_MASTER_API_KEY=Api-key" \
    -e "GALAXY_CONFIG_BRAND='Docker_galaxy_test'" \
    -e "GALAXY_LOGGING=full" \
    -e "GALAXY_CONFIG_HTTP=(VM-address)" \
    -e "GALAXY_CONFIG_SHED_TOOL_CONFIG_FILE=config/tool_sheds_conf.xml" \
    -e "GALAXY_CONFIG_TOOL_CONFIG_FILE=config/tool_conf.xml" \
    -e "GALAXY_CONFIG_TOOL_PATH=galaxy/tools/" \
    -e "GALAXY_CONFIG_CONDA_AUTO_INSTALL=true" \
    -e "GALAXY_CONFIG_CONDA_AUTO_INIT=true" \
    -v /tmp/:/tmp/ \
    -v /export/:/export \
    bgruening/galaxy-stable:18.05

Now when I run the script it is working until I get this error:

==> /home/galaxy/logs/uwsgi.log <==
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 818, in check
    raise ConfigurationError("Tool config file not found: %s" % path)
ConfigurationError: Tool config file not found: ./config/tool_conf.xml

Why it can’t see the tool_conf file even if the directory it’s correct?
Thank you for the help

2

please use an image >= 19.05, the 18.05 still use Ubuntu 14 now in EOF.
Check GitHub - bgruening/docker-galaxy-stable: Docker Images tracking the stable Galaxy releases.

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