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annotate venv/lib/python2.7/site-packages/planemo-0.16.0.dist-info/METADATA @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 Metadata-Version: 2.0
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2 Name: planemo
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3 Version: 0.16.0
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4 Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
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5 Home-page: https://github.com/galaxyproject/planemo
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6 Author: Galaxy Project and Community
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7 Author-email: jmchilton@gmail.com
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8 License: AFL
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9 Keywords: planemo
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10 Platform: UNKNOWN
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11 Classifier: Development Status :: 5 - Production/Stable
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12 Classifier: Intended Audience :: Developers
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13 Classifier: Environment :: Console
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14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
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15 Classifier: Operating System :: POSIX
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16 Classifier: Topic :: Software Development
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17 Classifier: Topic :: Software Development :: Code Generators
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18 Classifier: Topic :: Software Development :: Testing
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19 Classifier: Natural Language :: English
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20 Classifier: Programming Language :: Python :: 2
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21 Classifier: Programming Language :: Python :: 2.6
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22 Classifier: Programming Language :: Python :: 2.7
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23 Requires-Dist: Click
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24 Requires-Dist: six
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25 Requires-Dist: pyyaml
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26 Requires-Dist: jinja2
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27 Requires-Dist: docutils
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28 Requires-Dist: PyGithub
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29 Requires-Dist: bioblend
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30 Requires-Dist: glob2
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31
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32 .. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
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33 :alt: Planemo Logo
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34 :align: center
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35 :figwidth: 100%
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36 :target: https://github.com/galaxyproject/planemo
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37
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38 .. image:: https://readthedocs.org/projects/pip/badge/?version=latest
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39 :target: https://planemo.readthedocs.org
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40
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41 .. image:: https://badge.fury.io/py/planemo.svg
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42 :target: https://pypi.python.org/pypi/planemo/
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43
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44 .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
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45 :target: https://travis-ci.org/galaxyproject/planemo
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46
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47 .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master
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48 :target: https://coveralls.io/r/galaxyproject/planemo?branch=master
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49
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50
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51 Command-line utilities to assist in building and publishing Galaxy_ tools.
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52
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53 * Free software: Academic Free License version 3.0
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54 * Documentation: https://planemo.readthedocs.org.
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55 * Code: https://github.com/galaxyproject/planemo
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56
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57 Quick Start
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58 -----------
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59
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60 This quick start demonstrates using ``planemo`` commands to help
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61 develop Galaxy tools. Planemo can quickly be installed via
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62 Homebrew_ or as a more traditional Python project.
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63
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64 To install using Homebrew_ or linuxbrew_:
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65
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66 ::
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67
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68 brew tap galaxyproject/tap
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69 brew install planemo
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70
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71 For a more traditional Python installation simply setup a virtualenv
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72 for ``planemo`` (this example creates a new one in ``.venv``) and then
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73 install with ``pip``.
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74
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75 ::
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76
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77 % virtualenv .venv; . .venv/bin/activate
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78 % pip install planemo
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79
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80 Planemo is also available a `virtual appliance
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81 <https://planemo.readthedocs.org/en/latest/appliance.html>`_ for Docker_ or Vagrant_ (bundled
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82 with a preconfigured Galaxy server optimized for tool development).
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83
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84 This quick start will assume you will have a directory with one or more
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85 tool XML files. If none is available, one can be quickly create for
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86 demonstrating ``planemo`` as follows ``mkdir mytools; cd mytools; planemo
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87 project_init --template=demo``.
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88
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89 Planemo can check tools containing XML for common problems and best
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90 practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
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91 (also aliased as ``l``). ::
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92
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93 % planemo lint
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94 ...
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95
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96 Like many ``planemo`` commands - by default this will search the
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97 current directory and use all tool files it finds. It can be explicitly
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98 passed other tool files or a directory of tool files. ::
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99
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100 % planemo l randomlines.xml
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101
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102 The ``lint`` command takes in a additional options related to
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103 reporting levels, exit code, etc.... These options are descirbed here
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104 or (like all available commands) be accessed by passing it ``--help``.::
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105
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106 % planemo l --help
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107 Usage: planemo lint [OPTIONS] TOOL_PATH
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108 ...
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109
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110 Once tools are syntically correct - it is time to test. The ``test``
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111 `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
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112 can be used to test a tool or directory of tools.::
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113
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114 % planemo test --galaxy_root=../galaxy-central randomlines.xml
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115
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116 If no ``--galaxy_root`` is defined, ``planemo`` will check for a default in
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117 `~/.planemo.yml
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118 <http://planemo.readthedocs.org/en/latest/configuration.html>`_) and finally
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119 search the tool's parent directories for a Galaxy root directory (developing
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120 tools under Galaxy ``tools`` directory is a common development workflow).
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121 Planemo can also download and configure a disposable Galaxy instance just for
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122 testing by passing it ``-install_galaxy`` instead of a Galaxy root.::
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123
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124 % planemo t --install_galaxy
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125
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126 **Warning**: The features of Planemo that require a ``--galaxy_root`` will
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127 only work with Galaxy releases from 2015.
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128
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129 Planemo will create a HTML an output report in the current directory named
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130 ``tool_test_output.html`` (override with ``--test_output``). `Here <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_ is an
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131 example of such a report for Tophat.
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132
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133 Once tools have been linted and tested - the tools can be viewed in a
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134 Galaxy interface using the ``serve`` (``s``) `command
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135 <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.::
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136
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137 % planemo serve
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138
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139 Like ``test``, ``serve`` requires a Galaxy root and one can be
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140 explicitly specified with ``--galaxy_root`` or installed dynamically
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141 with ``--install_galaxy``.
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142
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143
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144 Experimental Features
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145 ---------------------
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146
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147 Planemo can also be used to explore some more experimental features related to
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148 Galaxy tooling - including support for `Travis CI`_, Docker_, Homebrew_.
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149
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150 -----------
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151 Tool Shed
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152 -----------
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153
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154 For information on using Planemo to publish artifacts to the Galaxy Tool Shed,
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155 check out the `Publishing to the Tool Shed`_ documentation on reathedocs.org.
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156
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157 -----------
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158 TravisCI
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159 -----------
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160
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161 When tools are ready to be published to GitHub_, it may be valuable to setup
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162 contineous integration to test changes committed and new pull requests.
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163 `Travis CI`_ is a service providing free testing and deep integration with
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164 GitHub_.
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165
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166 The ``travis_init`` `command
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167 <http://planemo.readthedocs.org/en/latest/commands.html#travis_init-
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168 command>`__ will bootstrap a project with files to ease contineous integration
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169 testing of tools using a Planemo driven approach inspired by this great `blog
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170 post <http://bit.ly/gxtravisci>`_ by `Peter Cock
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171 <https://github.com/peterjc>`_.
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172
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173 ::
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174
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175 % planemo travis_init .
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176 % # setup Ubuntu 12.04 w/tool dependencies
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177 % vim .travis/setup_custom_dependencies.bash
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178 % git add .travis.yml .travis
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179 % git commit -m "Add Travis CI testing infrastructure for tools."
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180 % git push # and register repository @ http://travis-ci.org/
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181
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182 In this example the file ``.travis/setup_custom_dependencies.bash`` should
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183 install the dependencies required to test your files on to the Travis user's
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184 ``PATH``.
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185
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186 This testing approach may only make sense for smaller repositories with a
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187 handful of tools. For larger repositories, such as `tools-devteam`_ or
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188 `tools-iuc`_ simply linting tool and tool shed artifacts may be more feasible.
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189 Check out the ``.travis.yml`` file used by the IUC as `example
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190 <https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml>`__.
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191
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192 -----------
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193 Docker
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194 -----------
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195
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196 Galaxy has `experimental support
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197 <https://wiki.galaxyproject.org/Admin/Tools/Docker>`_ for running jobs in
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198 Docker_ containers. Planemo contains tools to assist in development of Docker
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199 images for Galaxy tools.
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200
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201 A shell can be launched to explore the Docker enviornment referenced by tools
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202 that are annotated with publically registered Docker images.::
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203
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204 % $(planemo docker_shell bowtie2.xml)
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205
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206 For Docker containers still in development - a Dockerfile can be associated
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207 with a tool by sticking it in the tool's directory. Planemo can then build
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208 and tag a Docker image for this tool and launch a shell into it using the
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209 following commands.::
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210
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211 % planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
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212 % $(planemo docker_shell --from_tag bowtie2.xml)
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213
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214 For more details see the documentation for the `docker_build
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215 <http://planemo.readthedocs.org/en/latest/commands.html#docker_build-command>`__
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216 and `docker_shell
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217 <http://planemo.readthedocs.org/en/latest/commands.html#docker_shell-command>`__
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218 commands.
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219
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220 -----------
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221 Brew
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222 -----------
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223
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224 The Galaxy development team is exploring different options for integrating
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225 Homebrew_ and linuxbrew_ with Galaxy. One angle is resolving the tool requirements
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226 using ``brew``. An experimental approach for versioning of brew recipes will be
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227 used. See full discussion on the homebrew-science issues page here -
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228 https://github.com/Homebrew/homebrew-science/issues/1191. Information on the
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229 implementation can be found https://github.com/jmchilton/platform-brew until a
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230 more permanent project home is setup.
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231
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232 ::
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233
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234 % planemo brew_init # install linuxbrew (only need if not already installed)
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235 % planemo brew # install dependencies for all tools in directory.
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236 % planemo brew bowtie2.xml # install dependencies for one tool
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237 % which bowtie2
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238 bowtie2 not found
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239 % . <(planemo brew_env --shell bowtie2.xml) # shell w/brew deps resolved
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240 (bowtie2) % which bowtie2
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241 /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
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242 (bowtie2) % exit
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243 % . <(planemo brew_env bowtie2.xml) # or just source deps in cur env
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244 % which bowtie2
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245 /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
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246
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247 For more information see the documentation for the `brew
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248 <http://planemo.readthedocs.org/en/latest/commands.html#brew-command>`__
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249 and `brew_env
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250 <http://planemo.readthedocs.org/en/latest/commands.html#brew_env-command>`__ commands.
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251
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252 .. _Galaxy: http://galaxyproject.org/
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253 .. _GitHub: https://github.com/
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254 .. _Docker: https://www.docker.com/
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255 .. _Homebrew: http://brew.sh/
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256 .. _linuxbrew: https://github.com/Homebrew/linuxbrew
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257 .. _Vagrant: https://www.vagrantup.com/
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258 .. _Travis CI: http://travis-ci.org/
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259 .. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
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260 .. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
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261 .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
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262
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263
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264
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265
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266 History
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267 -------
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268
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269 .. to_doc
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270
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271 ---------------------
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272 0.16.0 (2015-10-07)
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273 ---------------------
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274
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275 * Adding new command ``dependency_script`` to convert Tool Shed dependencies
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276 into shell scripts - thanks to @peterjc.
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277 `Pull Request 310`_, f798c7e_, `Issue 303`_
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278 * Implement profiles in sheds section of the ``~/.planemo.yml``.
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279 `Pull Request 314`_
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280
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281 ---------------------
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282 0.15.0 (2015-10-01)
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283 ---------------------
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284
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285 * Template framework for reporting including new markdown and plain
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286 text reporting options for testing - thanks to @erasche.
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287 `Pull Request 304`_
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288 * XUnit style reporting for ``shed_diff`` command - thanks to
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289 @erasche. `Pull Request 305`_
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290 * Add new ``shed_build`` command for building repository tarballs -
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291 thanks to @kellrott. `Pull Request 297`_
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292 * Fix exit code handling for ``lint`` commands - thanks to @mvdbeek.
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293 `Pull Request 292`_
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294 * Improved documentation for ``serve`` command - thanks to @lparsons.
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295 `Pull Request 312`_
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296 * Tiny backward compatible Python 3 tweaks for tool factory - thanks
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297 to @peterjc. dad2d9d_
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298 * Fixed detection of virtual environment in ``Makefile`` - thanks to
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299 @lparsons. `Pull Request 311`_
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300 * Updates to Galaxy XSD - thanks to @mr-c. `Pull Request 309`_
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301 * Allow reading shed key option from an environment variable.
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302 `Pull Request 307`_
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303 * Allow specifying host to serve Galaxy using ``-host`` - thanks in
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304 part to @chambm. `Pull Request 301`_
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305 * Allow specifying defaults for ``-host`` and ``--port`` in
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306 ``~/.planemo.yml``. `Pull Request 301`_
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307 * Improve ``~/.planemo.yml`` sample comments - thanks to @martenson.
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308 `Pull Request 287`_
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309 * Update tool shed categories - thanks to @bgruening. `Pull Request 285`_
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310 * Improved output readibility for ``diff`` command - thanks to @martenson. `Pull Request 284`_
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311
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312 ---------------------
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313 0.14.0 (2015-08-06)
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314 ---------------------
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315
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316 * Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).
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317 `Pull Request 278`_
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318 * Fix ``tool_init`` command to use ``from_work_dir`` only if file in command
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319 (thanks to bug report and initial fix outline by Gildas Le Corguillé).
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320 `Pull Request 277`_
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321 * Various documentation fixes (thanks in part to Peter Cock and Daniel
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322 Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_,
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323 `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_
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324
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325 ---------------------
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326 0.13.2 (2015-07-06)
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327 ---------------------
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328
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329 * Fix project_init for missing files. cb5b906_
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330 * Various documentation improvements.
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331
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332 ---------------------
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333 0.13.1 (2015-07-01)
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334 ---------------------
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335
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336 * Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,
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337 f0610d7_
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338 * Fix tool linting for parameters that define an ``argument`` but not a
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339 ``name``. `Issue 245`_, aad1eed_
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340 * Many doc updates including a tutorial for developing tools in a test-driven
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341 fashion and instructions for using the planemo appliance through Kitematic
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342 (with Kitematic screenshots from Eric Rasche).
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343
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344 ---------------------
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345 0.13.0 (2015-06-28)
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346 ---------------------
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347
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348 * If planemo cannot find a Galaxy root, it will now automatically fetch
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349 one (specifing ``--galaxy_install`` will still force a fetch).
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350 `Pull Request 235`_
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351 * `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__
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352 has been updated to reflect new and vastly improved Docker and Vagrant
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353 virtual appliances are now available, as well as a new VirtualBox OVA
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354 variant.
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355 * Update linting for new tool XML features (including ``detect_errors``
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356 and output collections). `Issue 233`_, 334f2d4_
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357 * Fix ``shed_test`` help text. `Issue 223`_
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358 * Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_
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359 * Improvements to algorithm used to guess if an XML file is a tool XML file.
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360 `Issue 231`_
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361 * Fix configuration file handling bug. `Issue 240`_
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362
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363 ---------------------
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364 0.12.2 (2015-05-23)
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365 ---------------------
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366
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367 * Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.
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368 f3cafaa_
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369
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370 ---------------------
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371 0.12.1 (2015-05-21)
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372 ---------------------
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373
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374 * Fix to ensure the tab completion script is in the Python source tarball
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375 (required for setting up tab-completion for Homebrew). 6b4e7a6_
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376
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377 ---------------------
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378 0.12.0 (2015-05-21)
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379 ---------------------
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380
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381 * Implement a ``--failed`` flag for the ``test`` command to rerun
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382 previously faied tests. `Pull Request 210`_
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383 * Implement ``shed_update`` to upload contents and update repository
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384 metadata. `Pull Request 216`_
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385 * Implement ``shed_test`` and ``shed_serve`` commands to test and view
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386 published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_
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387 * Add shell tab-completion script. 37dcc07_
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388 * Many more commands allow specifing multiple tool and/or repository targets.
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389 `Issue 150`_
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390 * Add -m as alias for --message in planemo shed_upload (thanks to
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391 Peter Cock). `Pull Request 200`_
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392 * Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``
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393 files contain many repository. `Pull Request 215`_
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394 * More developer documentation, additional ``make`` targets including ones
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395 for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_
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396 * Small README improvement (thanks to Martin Čech) b53006d_
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397 * Fixes for shed operation error handling (thanks to Martin Čech).
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398 `Pull Request 203`_, `Pull Request 206`_
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399 * Fix for "smart" ``shed_diff`` not in the repository root directory
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400 (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_
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401 * Recursive ``shed_diff`` with directories not yet in Tool Shed.
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402 `Pull Request 208`_
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403 * Improve error handling and reporting for problematic ``--shed_target``
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404 values. `Issue 217`_
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405 * Fix typos in lint messages. `Issue 211`_
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406
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407
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408 ---------------------
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409 0.11.1 (2015-05-12)
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410 ---------------------
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411
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412 * Fix default behavior for ``planemo lint`` to use current directory if
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413 explicit paths are not supplied. 1e3668a_
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414
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415 ---------------------
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416 0.11.0 (2015-05-12)
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417 ---------------------
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418
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419 * More compact syntax for defining multiple custom inclusions in ``.shed.yml``
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420 files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,
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421 `Pull Request 196`_
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422 * Prevent ambigous destinations when defining custom inclusions in
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423 ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_
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424 * ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_
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425 * Handle empty tar-balls gracefully on older Python versions - thanks
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426 to Peter Cock. `Pull Request 187`_
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427 * Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_
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428 * Fix regression causing testing to no longer produce "pretty" test
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429 results under certain circumstances. `Issue 188`_
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430 * Fix for recursive ``shed_diff`` folder naming. `Issue 192`_
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431 * Fix output definitions to ``tool_init`` command. `Issue 189`_
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432
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433 ---------------------
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434 0.10.0 (2015-05-06)
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435 ---------------------
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436
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437 * Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml
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438 files. 8117e03_
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439 * Extend ``shed_lint`` to check for required files based on repository type.
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440 `Issue 156`_
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441 * Ignore common editor backup files during ``shed_upload``. `Issue 179`_
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442 * Fix missing file when installing from source via PyPI. `Issue 181`_
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443 * Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.
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444 8117e03_
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445 * Docstring fix thanks to @peterjc. fe7ad46_
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446
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447
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448 ---------------------
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449 0.9.0 (2015-05-03)
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450 ---------------------
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451
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452 * Add new logo to the README thanks to @petrkadlec from `puradesign.cz
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453 <http://puradesign.cz/en>`__ and @carlfeberhard from the Galaxy Project.
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454 `Issue 108`_
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455 * Implement smarter ``shed_diff`` command - it now produces a meaningful
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456 exit codes and doesn't report differences if these correspond to attributes
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457 that will be automatically populated by the Tool Shed. `Issue 167`_
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458 * Use new smarter ``shed_diff`` code to implement a new ``--check_diff``
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459 option for ``shed_upload`` - to check for meaningful differences before
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460 updating repositories. `Issue 168`_
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461 * Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is
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462 located in a git repository. `Issue 170`_
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463 * Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_
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464 * Fail if missing file inclusion statements encountered during ``.shed.yml``
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465 repository resolution - bug reported by @peterjc. `Issue 158`_
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466 * Improved exception handling for tool shed operations including new
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467 ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_
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468 * Implement more validation when using the ``shed_init`` command. 1cd0e2d_
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469 * Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff``
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470 commands and allow these commands to work with ``.shed.yml`` files defining
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471 multipe repositories. 40a1f57_
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472 * Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.
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473 15804be_
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474 * Fix problem introduced with ``setup.py`` during the 0.9.0 development cycle
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475 - thanks to @peterjc. `Pull Request 171`_
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476 * Fix clone bug introduced during 0.9.0 development cycle - thanks to
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477 @bgruening. `Pull Request 175`_
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478
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479 ---------------------
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480 0.8.4 (2015-04-30)
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481 ---------------------
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482
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483 * Fix for Travis CI testing picking up invalid tests (reported by @takadonet). `Issue 161`_
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484 * Fix tar ordering for consistency (always sort by name) - thanks to @peterjc. `Pull Request 164`_, `Issue 159`_
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485 * Fix exception handling related to tool shed operations - thanks to @peterjc. `Pull Request 155`_, b86fe1f_
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486
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487 ---------------------
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488 0.8.3 (2015-04-29)
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489 ---------------------
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490
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491 * Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.
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492 9ff0d2d_
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493 * Fix bug where planemo was producing tar files incompatible with the Tool
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494 Shed for package and suite repositories. a2ee135_
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495
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496 ---------------------
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497 0.8.2 (2015-04-29)
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498 ---------------------
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499
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500 * Fix bug with ``config_init`` command thanks to @bgruening. `Pull Request 151`_
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501 * Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by
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502 @peterjc. 9bf1eab_
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503
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504 ---------------------
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505 0.8.1 (2015-04-28)
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506 ---------------------
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507
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508 * Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
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509
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510 ---------------------
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511 0.8.0 (2015-04-27)
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512 ---------------------
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513
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514 * Implement the new ``shed_lint`` command that verifies various aspects of tool
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515 shed repositories - including XSD_ validation of ``repository_dependencies.xml``
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516 and ``tool_dependencies.xml`` files, best practices for README files, and the
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517 contents of ``.shed.yml`` files. This requires the lxml_ library to be available
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518 to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_
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519 `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_
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520 * Option to enable experimental XSD_ based validation of tools when ``lint``
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521 is executed with the new ``--xsd`` flag. This validation occurs against the
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522 unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__
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523 maintained by @JeanFred. This requires the lxml_ library to be
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524 available to Planemo or the application xmllint_ to be on its ``PATH``.
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525 `Pull Request 130`_ 912df02_
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526 * Allow skipping specific linters when using the ``lint`` command using the new
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527 ``--skip`` option. 26e3cdb_
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528 * Implement sophisticated options in ``.shed.yml`` to map a directory to many,
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529 custom Tool Shed repositories during shed operaitons such ``shed_upload``
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530 including automatically mapping tools to their own directories and automatically
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531 building suites repositories. `Pull Request 143`_
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532 * Make ``shed_upload`` more intelligent when building tar files so that package
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533 and suite repositories may have README files in source control and they will
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534 just be filtered out during upload. 53edd99_
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535 * Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``
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536 files in the specified directory. cc1a447_
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537 * Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``
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538 file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_
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539 * In addition to a single file or directory, allow ``lint`` to be passed multiple
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540 files. 343902d_ `Issue 139`_
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541 * Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_
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542 01f2af9_
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543 * Improved output formatting and option to write diffs to a file for the
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544 ``shed_diff`` command. 965511d_
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545 * Fix lint problem when using new Galaxy testing features such as expecting
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546 job failures and verifing job output. `Issue 138`_
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547 * Fix typo in ``test`` help thanks to first time contributor @pvanheus.
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548 `Pull Request 129`_ 1982076_
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549 * Fix NPE on empty ``help`` element when linting tools. `Issue 124`_
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550 * Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_
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551 * Fix for empty ``.shed.yml`` files. b7d9e96_
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552 * Fix the ``test`` command for newer versions of nose_. 33294d2_
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553 * Update help content and documentation to be clear ``normalize`` should not
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554 be used to update the contents of tool files at this time. 08de8de_
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555 * Warn on unknown ``command`` attributes when linting tools (anything but
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556 ``interpreter``). 4f61025_
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557 * Various design, documentation (including new documentation on Tool Shed
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558 `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),
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559 and testing related improvements (test coverage has risen from 65% to over
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560 80% during this release cycle).
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561
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562 ---------------------
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563 0.7.0 (2015-04-13)
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564 ---------------------
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565
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566 * Implement `shed_create` command to create Tool Shed repositories from
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567 ``.shed.yml`` files (thanks to Eric Rasche). `Pull Request 101`_
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568 * Allow automatic creation of missing repositories during ``shed_upload``
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569 with the new ``--force_repository_creation`` flag (thanks to Eric Rasche).
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570 `Pull Request 102`_
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571 * Allow specifying files to exclude in ``.shed.yml`` when creating tar files
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572 for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_
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573 * Resolve symbolic links when building Tool Shed tar files with
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574 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_
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575 * Add a `Contributor Code of Conduct
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576 <https://planemo.readthedocs.org/en/latest/conduct.html>`__.
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577 `Pull Request 113`_
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578 * Omit ``tool_test_output.json`` from Tool Shed tar file created with
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579 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_
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580 * Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.
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581 * Initial work on implementing tests cases for Tool Shed functionality.
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582 182fe57_
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583 * Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
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584 * Download Galaxy from the new, official Github repository. 7c69bf6_
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585 * Update travis_test to install stable planemo from PyPI. 39fedd2_
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586 * Enable caching on ``--install_galaxy`` by default (disable with
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587 ``--no_cache_galaxy``). d755fe7_
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588
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589 ---------------------
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590 0.6.0 (2015-03-16)
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591 ---------------------
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592
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593 * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
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594 * Fix ``tool_init`` to quote file names (thanks to Peter Cock). `Pull Request 98`_.
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595 * Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_
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596 * Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_
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597 * Add linting of tag order for tool XML files. 4823c5e_
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598 * Add linting of ``stdio`` tags in tool XML files. 8207026_
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599 * More tests, much higher test coverage. 0bd4ff0_
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600
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601 ---------------------
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602 0.5.0 (2015-02-22)
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603 ---------------------
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604
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605 * Implement ``--version`` option. `Issue 78`_
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606 * Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to
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607 persist temp files. 2e41e0a_
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608 * Fix bug that left temp files undeleted. `Issue 80`_
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609 * More improvements to release process. fba3874_
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610
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611 ---------------------
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612 0.4.2 (2015-02-21)
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613 ---------------------
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614
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615 * Fix setup.py for installing non-Python data from PyPI (required newer
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616 for ``tool_factory`` command and reStructuredText linting). Thanks to
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617 Damion Dooley for the bug report. `Issue 83`_
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618
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619 ---------------------
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620 0.4.1 (2015-02-16)
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621 ---------------------
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622
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623 * Fix README.rst so it renders properly on PyPI.
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624
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625 ---------------------
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626 0.4.0 (2015-02-16)
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627 ---------------------
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628
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629 * Implement ``tool_init`` command for bootstrapping creation of new
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630 tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
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631 * Implement ``normalize`` command for reorganizing tool XML and macro
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632 debugging. e8c1d45_
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633 * Implement ``tool_factory`` command to spin up Galaxy pre-configured the
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634 `Tool Factory
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635 <http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf>`_. 9e746b4_
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636 * Added basic linting of ``command`` blocks. b8d90ab_
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637 * Improved linting of ``help`` blocks, including verifying valid
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638 `reStructuredText`. 411a8da_
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639 * Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
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640 * Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
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641 * Add additional dependencies to ``setup.py`` more functionality works out
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642 of the box. 85b9614_
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643 * Fix terrible error message related to ``bioblend`` being unavailable.
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644 `Issue 70`_
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645 * Various smaller documentation and project structure improvements.
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646
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647 ---------------------
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648 0.3.1 (2015-02-15)
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649 ---------------------
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650
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651 * Fixes to get PyPI workflow working properly.
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652
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653 ---------------------
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654 0.3.0 (2015-02-13)
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655 ---------------------
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656
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657 * Add option (``-r``) to the ``shed_upload`` command to recursively upload
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658 subdirectories (thanks to Eric Rasche). `Pull Request 68`_
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659 * Fix diff formatting in test reports (thanks to Eric Rasche).
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660 `Pull Request 63`_
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661 * Grab updated test database to speed up testing (thanks to approach from
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662 Eric Rasche and Dannon Baker). `Issue 61`_, dff4f33_
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663 * Fix test data command-line argument name (was ``test-data`` now it is
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664 ``test_data``). 834bfb2_
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665 * Use ``tool_data_table_conf.xml.sample`` file if
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666 ``tool_data_table_conf.xml.test`` is unavailable. Should allow some
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667 new tools to be tested without modifying Galaxy's global
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668 ``tool_data_table_conf.xml`` file. ac4f828_
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669
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670 ---------------------
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671 0.2.0 (2015-01-13)
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672 ---------------------
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673
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674 * Improvements to way Planemo loads its own copy of Galaxy modules to prevent
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675 various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
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676 * Allow setting various test output options in ``~/.planemo.yml`` and disabling
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677 JSON output. 21bb463_
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678 * More experimental Brew and Tool Shed options that should not be considered
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679 part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
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680 * Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
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681 report.) a4110a8_
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682 * Documentation fixes for tool linting command (thanks to Nicola Soranzo).
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683 `Pull Request 51`_
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684
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685 ---------------------
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686 0.1.0 (2014-12-16)
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687 ---------------------
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688
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689 * Moved repository URL to https://github.com/galaxyproject/planemo.
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690 * Support for publishing to the Tool Shed. `Pull Request 6`_
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691 * Support for producing diffs (``shed_diff``) between local repositories and
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692 the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
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693 * Use tool's local test data when available - add option for configuring
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694 ``test-data`` target. `Pull Request 1`_
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695 * Support for testing tool features dependent on cached data. 44de95c_
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696 * Support for generating XUnit tool test reports. 82e8b1f_
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697 * Prettier HTML reports for tool tests. 05cc9f4_
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698 * Implement ``share_test`` command for embedding test result links in pull
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699 requests. `Pull Request 40`_
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700 * Fix for properly resolving links during Tool Shed publishing (thanks to Dave
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701 Bouvier). `Pull Request 29`_
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702 * Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
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703 * Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
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704 Blankenberg). a2c13e4_
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705 * Automate more of Travis CI testing so the scripts added to tool repository
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706 can be smaller. 20a8680_
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707 * Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
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708 `Pull Request 23`_
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709 * Various documentation fixes (thanks to Martin Čech). 36f7cb11_, b9232e55_
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710 * Various smaller fixes for Docker support, tool linting, and documentation.
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711
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712 ---------------------
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713 0.0.1 (2014-10-04)
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714 ---------------------
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715
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716 * Initial work on the project - commands for testing, linting, serving Galaxy
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717 tools - and more experimental features involving Docker and Homebrew. 7d07782_
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718
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719 .. github_links
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720 .. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e
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721 .. _Issue 303: https://github.com/galaxyproject/planemo/issues/303
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722 .. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310
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723 .. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314
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724 .. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d
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725 .. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312
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726 .. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311
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727 .. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309
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728 .. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
729 .. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
730 .. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
731 .. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
732 .. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
733 .. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
734 .. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
735 .. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
736 .. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
737 .. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
738 .. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
739 .. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
740 .. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
741 .. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
742 .. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
743 .. _Issue 272: https://github.com/galaxyproject/planemo/issues/272
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
744 .. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
745 .. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
746 .. _Issue 243: https://github.com/galaxyproject/planemo/issues/243
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
747 .. _Issue 245: https://github.com/galaxyproject/planemo/issues/245
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
748 .. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
749 .. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
750 .. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
751 .. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
752 .. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
753 .. _Issue 223: https://github.com/galaxyproject/planemo/issues/223
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
754 .. _Issue 231: https://github.com/galaxyproject/planemo/issues/231
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
755 .. _Issue 233: https://github.com/galaxyproject/planemo/issues/233
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
756 .. _Issue 240: https://github.com/galaxyproject/planemo/issues/240
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
757 .. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
758 .. _6b4e7a6: https://github.com/galaxyproject/planemo/commit/6b4e7a6
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
759 .. _Issue 176: https://github.com/galaxyproject/planemo/issues/176
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
760 .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
761 .. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
762 .. _Issue 150: https://github.com/galaxyproject/planemo/issues/150
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
763 .. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
764 .. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
765 .. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
766 .. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
767 .. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
768 .. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
769 .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
770 .. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
771 .. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
772 .. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
773 .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
774 .. _Issue 217: https://github.com/galaxyproject/planemo/issues/217
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
775 .. _Issue 211: https://github.com/galaxyproject/planemo/issues/211
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
776 .. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
777 .. _Issue 209: https://github.com/galaxyproject/planemo/issues/209
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
778 .. _Issue 206: https://github.com/galaxyproject/planemo/issues/206
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
779 .. _Issue 205: https://github.com/galaxyproject/planemo/issues/205
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
780 .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
781 .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
782 .. _Issue 180: https://github.com/galaxyproject/planemo/issues/180
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
783 .. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
784 .. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
785 .. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
786 .. _Issue 186: https://github.com/galaxyproject/planemo/issues/186
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
787 .. _Issue 188: https://github.com/galaxyproject/planemo/issues/188
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
788 .. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
789 .. _Issue 192: https://github.com/galaxyproject/planemo/issues/192
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
790 .. _Issue 189: https://github.com/galaxyproject/planemo/issues/189
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
791 .. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
792 .. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
793 .. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
794 .. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
795 .. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
796 .. _Issue 156: https://github.com/galaxyproject/planemo/issues/156
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
797 .. _Issue 179: https://github.com/galaxyproject/planemo/issues/179
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
798 .. _Issue 181: https://github.com/galaxyproject/planemo/issues/181
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
799 .. _Issue 114: https://github.com/galaxyproject/planemo/issues/114
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
800 .. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
801 .. _Issue 108: https://github.com/galaxyproject/planemo/issues/108
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
802 .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
803 .. _Issue 158: https://github.com/galaxyproject/planemo/issues/158
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
804 .. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
805 .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
806 .. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
807 .. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
808 .. _Issue 167: https://github.com/galaxyproject/planemo/issues/167
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
809 .. _Issue 170: https://github.com/galaxyproject/planemo/issues/170
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
810 .. _Issue 169: https://github.com/galaxyproject/planemo/issues/169
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
811 .. _Issue 168: https://github.com/galaxyproject/planemo/issues/168
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
812 .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
813 .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
814 .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
815 .. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
816 .. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
817 .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
818 .. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
819 .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
820 .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
821 .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
822 .. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
823 .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
824 .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
825 .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
826 .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
827 .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
828 .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
829 .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
830 .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
831 .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
832 .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
833 .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
834 .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
835 .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
836 .. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
837 .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
838 .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
839 .. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
840 .. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
841 .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
842 .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
843 .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
844 .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
845 .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
846 .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
847 .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
848 .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
849 .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
850 .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
851 .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
852 .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
853 .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
854 .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
855 .. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
856 .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
857 .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
858 .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
859 .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
860 .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
861 .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
862 .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
863 .. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
864 .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
865 .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
866 .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
867 .. _Issue 78: https://github.com/galaxyproject/planemo/issues/78
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
868 .. _Issue 80: https://github.com/galaxyproject/planemo/issues/80
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
869
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
870
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
871 .. _Issue 83: https://github.com/galaxyproject/planemo/issues/83
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
872 .. _Issue 70: https://github.com/galaxyproject/planemo/issues/70
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
873 .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
874 .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
875 .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
876 .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
877 .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
878 .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
879 .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
880 .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
881 .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
882 .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
883 .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
884 .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
885
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
886 .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
887 .. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
888 .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
889 .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
890 .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
891 .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
892 .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
893 .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
894 .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
895 .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
896 .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
897 .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
898 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
899 .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
900 .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
901 .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
902 .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
903 .. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
904 .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
905 .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
906 .. _7d07782: https://github.com/galaxyproject/planemo/commit/7d077828559c9c9c352ac814f9e3b86b1b3a2a9f
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
907 .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
908 .. _36f7cb11: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
909 .. _b9232e55: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
910
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
911 .. _bioblend: https://github.com/galaxyproject/bioblend/
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
912 .. _XSD: http://www.w3schools.com/schema/
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
913 .. _lxml: http://lxml.de/
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
914 .. _xmllint: http://xmlsoft.org/xmllint.html
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
915 .. _nose: https://nose.readthedocs.org/en/latest/
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
916
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
917