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https://github.com/pjbriggs/nebulizer

Command line utilities to help manage users, tools and data libraries in a Galaxy instance via the API
https://github.com/pjbriggs/nebulizer

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Command line utilities to help manage users, tools and data libraries in a Galaxy instance via the API

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   :target: https://github.com/pjbriggs/nebulizer



Command-line utilities to help with managing users, data libraries and

tools in a `Galaxy `_ instance, using the

Galaxy API via the `Bioblend `_

library.



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   :target: https://nebulizer.readthedocs.io



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* 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 `_.



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 `_:



 * ``list_users``

 * ``create_user``

 * ``create_batch_users``

 * ``create_users_from_file``

 * ``delete_user``



`Managing data libraries `_:



 * ``list_libraries``

 * ``create_library``

 * ``create_library_folder``

 * ``add_library_datasets``



`Managing tools `_:



 * ``list_tools``

 * ``list_tool_panel``

 * ``install_tool``

 * ``update_tool``

 * ``uninstall_tool``

 * ``search_toolshed``



`Managing quotas `_:



 * ``quotas``

 * ``quota_add``

 * ``quota_mod``

 * ``quota_del``



`Querying Galaxy instances `_:



 * ``ping`` (check if a Galaxy instance is alive)

 * ``config`` (fetch configuration for a Galaxy instance)



See the `tutorial `_

for a walkthrough some of these commands.



------------

Contributors

------------



Nebulizer has been developed by Peter Briggs @pjbriggs, with

contributions from:



 * Hugo van Kemenade (`@hugovk `_)



Thanks to Peter van Heuseden (`@pvanheus `_)

for porting Nebulizer into Bioconda.