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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
Last synced: 3 months ago
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Command line utilities to help manage users, tools and data libraries in a Galaxy instance via the API
- Host: GitHub
- URL: https://github.com/pjbriggs/nebulizer
- Owner: pjbriggs
- License: other
- Created: 2015-09-04T09:02:55.000Z (about 9 years ago)
- Default Branch: devel
- Last Pushed: 2021-08-03T11:41:27.000Z (over 3 years ago)
- Last Synced: 2024-05-17T15:21:05.142Z (6 months ago)
- Language: Python
- Size: 696 KB
- Stars: 6
- Watchers: 4
- Forks: 1
- Open Issues: 22
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.rst
- License: LICENSE
Awesome Lists containing this project
- awesome-galaxy - nebulizer - Command-line utilities to help with managing users, data libraries and tools in a Galaxy instance
README
.. figure:: https://raw.githubusercontent.com/pjbriggs/nebulizer/master/docs/nebulizer_logo.png
:alt: Nebulizer Logo
:align: center
:figwidth: 100%
:target: https://github.com/pjbriggs/nebulizerCommand-line utilities to help with managing users, data libraries and
tools in a `Galaxy `_ instance, using the
Galaxy API via the `Bioblend `_
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://github.com/pjbriggs/nebulizer/workflows/Python%20CI/badge.svg
:target: https://github.com/pjbriggs/nebulizer/actions?query=workflow%3A%22Python+CI%22* 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 nebulizerThis 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.