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        "author": "",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: End Users/Desktop",
            "Intended Audience :: System Administrators",
            "License :: OSI Approved :: Academic Free License (AFL)",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": ".. figure:: https://raw.githubusercontent.com/pjbriggs/nebulizer/master/docs/nebulizer_logo.png\n   :alt: Nebulizer Logo\n   :align: center\n   :figwidth: 100%\n   :target: https://github.com/pjbriggs/nebulizer\n\nCommand-line utilities to help with managing users, data libraries and\ntools in a `Galaxy <https://galaxyproject.org/>`_ instance, using the\nGalaxy API via the `Bioblend <http://bioblend.readthedocs.org/en/latest/>`_\nlibrary.\n\n.. image:: https://readthedocs.org/projects/pip/badge/?version=latest\n   :target: https://nebulizer.readthedocs.io\n\n.. image:: https://badge.fury.io/py/nebulizer.svg\n   :target: https://pypi.python.org/pypi/nebulizer/\n\n.. image:: https://travis-ci.org/pjbriggs/nebulizer.png?branch=master\n   :target: https://travis-ci.org/pjbriggs/nebulizer\n\n* Free software: Academic Free License version 3.0\n* Documentation: https://nebulizer.readthedocs.io\n* Code: https://github.com/pjbriggs/nebulizer\n\n.. warning::\n\n   **CAVEAT** ``nebulizer`` is still a work in progress; please exercise\n   caution when attempting irreversible operations especially against\n   production Galaxy instances (for example when creating users or data\n   libraries).\n\nQuick Start\n-----------\n\nThis quick start gives some examples of using ``nebulizer`` commands\nto perform remote administration tasks on a Galaxy instance from the\ncommand line.\n\n-----------------\nGetting Nebulizer\n-----------------\n\nIt is recommended to install Nebulizer via ``pip`` in a virtualenv,\nfor example::\n\n  % virtualenv .venv; . .venv/bin/activate\n  % pip install nebulizer\n\nThis will provide an executable called ``nebulizer`` with a number\nof subcommands for performing different tasks remotely on Galaxy\ninstances.\n\n----------------\nNebulizer Basics\n----------------\n\nTo interact remotely with a Galaxy instance using Nebulizer requires\nat minimum the URL of the instance and then either an API key or a\nuser login name.\n\nFor example to list data libraries available on Galaxy Main::\n\n  % nebulizer -k 9b376af2250818d14949b3c list_libraries https://usegalaxy.org\n\nor::\n\n  % nebulizer -u peter.briggs@manchester.ac.uk list_libraries https://usegalaxy.org\n\n(in this second case ``nebulizer`` will prompt for the Galaxy\npassword to authenticate the user login.)\n\nSpecifying full API keys and Galaxy URLs each time a command is run\nis tedious, so Nebulizer can store URL-key pairs locally to make this\neasier.\n\nFor example to store the API key for Galaxy main::\n\n  % nebulizer add_key main https://usegalaxy.org 9b376af2250818d14949b3c\n\nstores the API key and URL pair and associates it with the alias ``main``.\n\nAlternatively Nebulizer can fetch the API key itself if the user\nlogin is provided instead, for example::\n\n  % nebulizer -u peter.briggs@manchester.ac.uk add_key main https://usegalaxy.org\n\nThe stored alias can then be used as a substitute for the URL with the\nthe stored API key being fetched behind the scenes. Then to list the\ndata libraries again it is sufficient to do just::\n\n  % nebulizer list_libraries main\n\nTo find out which user is associated with an alias do::\n\n  % nebulizer whoami main\n\nThe following sections contain examples of how Nebulizer might be\nused to perform various administrive tasks.\n\n--------------\nManaging Users\n--------------\n\nList users matching specific name::\n\n  nebulizer list_users galaxy --name=\"*briggs*\"\n\nAdd a new user::\n\n  nebulizer create_user galaxy -p pa55w0rd a.non@galaxy.org\n\n-----------------------\nManaging Data Libraries\n-----------------------\n\nList data libraries::\n\n  nebulizer list_libraries galaxy\n\nCreate a data library called ``NGS data`` and a subfolder ``Run 21``::\n\n  nebulizer create_library galaxy \\\n    --description=\"Sequencing data analysed in 2015\" \"NGS data\"\n  nebulizer create_library_folder localhost \"NGS data/Run 21\"\n\nList contents of this folder::\n\n  nebulizer list_libraries galaxy \"NGS data/Run 21\"\n\nUpload files to it from the local system::\n\n  nebulizer add_library_datasets galaxy \"NGS data/Run 21\" ~/Sample1_R*.fq\n\nAdd a file which is on the Galaxy server filesystem to a library as a\nlink::\n\n  nebulizer add_library_datasets galaxy --server --link \"NGS data/fastqs\" \\\n    /galaxy/hosted_data/example.fq\n\n--------------\nManaging Tools\n--------------\n\nList all tools that are available in a Galaxy instance::\n\n  nebulizer list_tools galaxy\n\nList all the ``cuff...`` tools that were installed from a toolshed::\n\n  nebulizer list_tools galaxy --name=\"cuff*\" --installed\n\nList all the tool repositories that are installed along with the tools\nthat they provide::\n\n  nebulizer list_installed_tools localhost --list-tools\n\nList all the tool repositories that have available updates or upgrades::\n\n  nebulizer list_installed_tools localhost --updateable\n\nInstall the most recent FastQC from the main toolshed::\n\n  nebulizer install_tool localhost \\\n    --tool-panel-section=\"NGS: QC and manipulation\" \\\n    toolshed.g2.bx.psu.edu devteam fastqc\n\nUpdate FastQC tool to latest installable revision::\n\n  nebulizer update_tool localhost toolshed.g2.bx.psu.edu devteam fastqc\n\n.. warning::\n\n   By default checks on the availability of updates for tools\n   performed by the ``list_installed_tools`` and ``update_tool``\n   commands are done using information cached by the Galaxy\n   instance in question. As a result these commands may not\n   always indicate when updates are available.\n\n   To force these commands to check the installed revisions\n   against those in the toolshed, add the ``--check-toolshed``\n   option. Note however that this can impose a significant\n   overhead which can make the commands much slower.\n\n----------------------------------\nChecking status of a Galaxy server\n----------------------------------\n\n'Ping' a Galaxy instance to check it's alive and responding to\nrequests::\n\n    nebulizer ping localhost\n\nCommands\n--------\n\nAll functionality is available as subcommands of the ``nebulizer``\nutility.\n\n---------------\nUser Management\n---------------\n\n * ``list_users``: List users in Galaxy instance.\n * ``create_user``: Create new Galaxy user.\n * ``create_batch_users``: Create multiple Galaxy users from a template.\n * ``create_users_from_file``: Create multiple Galaxy users from a file.\n\n-----------------------\nData Library Management\n-----------------------\n\n * ``list_libraries``:  List data libraries and contents.\n * ``create_library``: Create new data library.\n * ``create_library_folder``: Create new folder in a data library.\n * ``add_library_datasets``: Add datasets to a data library.\n\n---------------\nTool Management\n---------------\n\n * ``list_tools``: List tools in Galaxy instance.\n * ``list_tool_panel``: List tool panel contents.\n * ``list_installed_tools``: List installed tool repositories.\n * ``install_tool``: Install tool from toolshed.\n\n-------------------------------\nBulk Tool Repository Management\n-------------------------------\n\n * ``list_repositories``: List installed tool repos for (re)install.\n * ``install_repositories``: Install tool repositories listed in a file.\n\n------------------------\nLocal API Key Management\n------------------------\n\n * ``add_key``: Store new Galaxy URL and API key.\n * ``list_keys``: List stored Galaxy API keys.\n * ``remove_key``: Remove stored Galaxy API key.\n * ``update_key``: Update stored Galaxy API key.\n\n--------------\nOther commands\n--------------\n\n * ``ping``: 'Ping' a Galaxy instance.\n * ``whoami``: Print user details associated with API key.\n\nHints and Tips\n--------------\n\n------------------------\nManaging Galaxy API keys\n------------------------\n\nNebulizer stores the URL-key pairs in the file ``.nebulizer``\nlocated in the user's home directory. This file consists of\ntab-delimited lines with the following columns::\n\n  alias|Galaxy_URL|API_key\n\nThis file can be edited by hand using a text editor such as\n``vi``; however Nebulizer provides a set of commands for\nquerying and modifying the file contents.\n\nTo list the stored aliases with associated Galaxy URLs and\nAPI keys::\n\n  % nebulizer list_keys\n\nTo add a new alias called 'production' for a Galaxy instance::\n\n  nebulizer add_key production http:://galaxy.org/ 5e7a1264905c8f0beb80002f7de13a40\n\nUpdate the API key for 'production'::\n\n  nebulizer update_key production --new-api-key=37b6430624255b8c61a137abd69ae3bb\n\nRemove the entry for 'production'::\n\n  nebulizer remove_key production\n\nMultiple URL-key pairs can be stored; only the associated\naliases need to be unique. For example::\n\n  % nebulizer -u admin@galaxy.org add_key palfinder https://palfinder.ls.manchester.ac.uk\n  ...prompt for password...\n  % nebulizer list_libraries palfinder\n\n----------------------------------------------\nHandling SSL Certificate Verification Failures\n----------------------------------------------\n\nNebulizer commands will fail for Galaxy instances which are served over\n``https`` protocol without a valid SSL certificate, reporting an error like::\n\n  [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590), 0 attempts left: None\n\nIn this case adding the ``--no-verify`` (``-n``) option turns off the\ncertificate verification and should enable a connection to be made.\n\n---------------------------------------------------------\nAccessing Galaxy with Email & Password instead of API key\n---------------------------------------------------------\n\nIt is possible to use your normal Galaxy login credentials (i.e. your email\nand password) to access the API on a Galaxy instance without using the\nAPI key, using the ``-u``/``--username`` option, e.g.::\n\n  nebulizer -u joe.bloggs@example.com list_libraries \"NGS data/Run 21\"\n\nYou will be prompted to enter the password; however you can also use the\n``-P``/``--galaxy_password`` option to specify it explicitly on the command\nline.\n\n-------------------------------------------------\nInstalling Multiple Tool Repositories from a List\n-------------------------------------------------\n\nIt is possible to install a list of tool repositories into a\nGalaxy instance by using the ``install_repositories`` command::\n\n  nebulizer install_repositories galaxy tools.tsv\n\nThe ``tools.tsv`` file must be a tab-delimited list of repositories,\none repository per line in the format::\n\n  TOOLSHED|OWNER|REPOSITORY|REVISON|SECTION\n\nFor example::\n\n  toolshed.g2.bx.psu.edu\tdevteam\tbowtie_wrappers\t9ca609a2a421\tNGS: Mapping\n\nA list of tool repositories already installed in a Galaxy instance\ncan be generated in this format using the ``list_repositories``\ncommand::\n\n  nebulizer list_repositories galaxy > tools.tsv\n\nIn principle the combination of these two commands can be used to\n'clone' the installed tools from one Galaxy instance into another.\n\nFor example to replicate the tools installed on the 'Palfinder'\ninstance::\n\n  nebulizer list_repositories https://palfinder.ls.manchester.ac.uk > palfinder.tsv\n  nebulizer install_repositories http://127.0.0.1 palfinder.tsv\n\nDeprecated Utilities\n--------------------\n\nThe following additional utilities are included for backwards\ncompatibility but are deprecated and likely to be removed in a\nfuture version:\n\n * ``manage_users``: list and create user accounts\n * ``manage_libraries``: list, create and populate data libraries\n * ``manage_tools``: list and install tools from toolsheds\n\nThey are not documented further here.\n\nLicense\n-------\n\nNebulizer is licensed under the `Academic Free License (AFL) <https://opensource.org/licenses/AFL-3.0>`_.",
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