Metadata-Version: 2.1
Name: nebulizer
Version: 0.7.0
Summary: CLI for remote admin of Galaxy servers
Home-page: https://github.com/pjbriggs/nebulizer
Maintainer: Peter Briggs
Maintainer-email: peter.briggs@manchester.ac.uk
License: AFL
Description: .. figure:: https://raw.githubusercontent.com/pjbriggs/nebulizer/master/docs/nebulizer_logo.png
           :alt: Nebulizer Logo
           :align: center
           :figwidth: 100%
           :target: https://github.com/pjbriggs/nebulizer
        
        Command-line utilities to help with managing users, data libraries and
        tools in a `Galaxy <https://galaxyproject.org/>`_ instance, using the
        Galaxy API via the `Bioblend <https://bioblend.readthedocs.io/en/latest/>`_
        library.
        
        .. image:: https://readthedocs.org/projects/pip/badge/?version=latest
           :target: https://nebulizer.readthedocs.io
        
        .. image:: https://badge.fury.io/py/nebulizer.svg
           :target: https://pypi.python.org/pypi/nebulizer/
        
        .. image:: https://travis-ci.org/pjbriggs/nebulizer.svg?branch=master
            :target: https://travis-ci.org/pjbriggs/nebulizer
        
        * Free software: Academic Free License version 3.0
        * Documentation: https://nebulizer.readthedocs.io
        * Code: https://github.com/pjbriggs/nebulizer
        
        .. note::
        
           **Nebulizer is still a work in progress.**
        
           Please exercise caution when attempting irreversible operations,
           especially against production Galaxy instances (for example when
           creating users or data libraries).
        
        Quick Start
        -----------
        
        This quick start gives some examples of using ``nebulizer`` commands
        to perform remote administration tasks on a Galaxy instance from the
        command line.
        
        -----------------
        Getting Nebulizer
        -----------------
        
        It is recommended to install Nebulizer via ``pip`` in a virtualenv,
        for example:
        
        ::
        
          % virtualenv .venv
          % source .venv/bin/activate
          % pip install nebulizer
        
        This will provide an executable called ``nebulizer`` with a number
        of subcommands for performing different tasks remotely on Galaxy
        instances.
        
        ----------------
        Nebulizer Basics
        ----------------
        
        Generally Nebulizer commands take the form:
        
        ::
        
           nebulizer COMMAND GALAXY [OPTIONS]
        
        To interact remotely with a Galaxy instance using Nebulizer requires
        at minimum the URL of the instance and then either an API key or a
        user login name.
        
        For example to list the data libraries available on Galaxy Main:
        
        ::
        
          nebulizer -k 9b376af2250818d14949b3c list_libraries https://usegalaxy.org
        
        or
        
        ::
        
          nebulizer -u USER@DOMAIN list_libraries https://usegalaxy.org
        
        In this second case Nebulizer will prompt for the Galaxy
        password to authenticate the user login, unless it's supplied via
        the ``-P`` option.
        
        To store the Galaxy URL-API key pair against an alias ``main``, to
        avoid needing full authentication details each time:
        
        ::
        
          nebulizer add_key main https://usegalaxy.org 9b376af2250818d14949b3c
        
        or alternatively get Nebulizer to fetch the API key itself by
        supplying the user login:
        
        ::
        
          nebulizer -u USER@DOMAIN add_key main https://usegalaxy.org
        
        More information on managing API keys in Nebulizer can found
        `here <https://nebulizer.readthedocs.io/en/latest/managing_keys.html>`_.
        
        The stored alias is then used in subsequent commands, for example
        to list the data libraries again it is now sufficient to do just:
        
        ::
        
          nebulizer list_libraries main
        
        The following sections contain examples of how Nebulizer might be
        used to perform various administrive tasks.
        
        Nebulizer provides subcommands to perform various administrive tasks:
        
        `Managing users <https://nebulizer.readthedocs.io/en/latest/users.html>`_:
        
         * ``list_users``
         * ``create_user``
         * ``create_batch_users``
         * ``create_users_from_file``
         * ``delete_user``
        
        `Managing data libraries <https://nebulizer.readthedocs.io/en/latest/libraries.html>`_:
        
         * ``list_libraries``
         * ``create_library``
         * ``create_library_folder``
         * ``add_library_datasets``
        
        `Managing tools <https://nebulizer.readthedocs.io/en/latest/tools.html>`_:
        
         * ``list_tools``
         * ``list_tool_panel``
         * ``install_tool``
         * ``update_tool``
         * ``uninstall_tool``
         * ``search_toolshed``
        
        `Managing quotas <https://nebulizer.readthedocs.io/en/latest/quotas.html>`_:
        
         * ``quotas``
         * ``quota_add``
         * ``quota_mod``
         * ``quota_del``
        
        `Querying Galaxy instances <https://nebulizer.readthedocs.io/en/latest/querying_galaxy.html>`_:
        
         * ``ping`` (check if a Galaxy instance is alive)
         * ``config`` (fetch configuration for a Galaxy instance)
        
        See the `tutorial <https://nebulizer.readthedocs.io/en/latest/users.html>`_
        for a walkthrough some of these commands.
        
        ------------
        Contributors
        ------------
        
        Nebulizer has been developed by Peter Briggs @pjbriggs, with
        contributions from:
        
         * Hugo van Kemenade (`@hugovk <https://github.com/hugovk>`_)
        
        Thanks to Peter van Heuseden (`@pvanheus <https://github.com/pvanheus>`_)
        for porting Nebulizer into Bioconda.
        
Platform: Posix; MacOS X; Windows
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: System Administrators
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Academic Free License (AFL)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.6
