docker-galaxy-stable: Can't create /export/ftp

When I start galaxy-stable:dev (image id 21f0db53e900 2016-08-16 maybe this) container following command

mkdir export
chmod 777 export
docker run  -e NONUSE="condor" -v $PWD/export:/export --rm bgruening/galaxy-stable:dev

It has error

DEBUG:galaxy.app:python path is: lib/, ., , /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
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 55, in paste_app_factory
    app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "lib/galaxy/app.py", line 48, in __init__
    self.config.check()
  File "lib/galaxy/config.py", line 658, in check
    self._ensure_directory( path )
  File "lib/galaxy/config.py", line 639, in _ensure_directory
    raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) )
ConfigurationError: Unable to create missing directory: /export/ftp

Currently

GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/ftp

Some previous version

GALAXY_CONFIG_FTP_UPLOAD_DIR=/export/galaxy-central/database/ftp

I think it need to create directory and set owner and permission in _/usr/bin/startup_ or _/usr/local/bin/export_user_files.py_

I set mode 777 to $PWD/export But after the container start $PWD/export has 755 I think it is set at _/usr/local/bin/export_user_files.py_ L114 ansible-galaxy-extras/export_user_files.py.j2 at 17de3fb4356c2efd1259d7d12b558bc361ab7316 · galaxyproject/ansible-galaxy-extras

About this issue

  • Original URL
  • State: closed
  • Created 8 years ago
  • Comments: 22 (22 by maintainers)

Most upvoted comments

Thanks for testing! Very much appreciated! Dev has a lot of changes so any feedback is more then welcome. Let me know if you encounter anything else, or any feature you are missing. I will go and close all issues and PRs.

Thanks again!

I think I know what it is, I’m currently not sure how to fix it in a nice way. Yesterday I got the monolithic container working, but the compose one broke. Will think about it!

Thanks @manabuishii!