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1 # WARNING before you start
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2 # Install this tool on a private Galaxy ONLY
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3 # Please NEVER on a public or production instance
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4 # updated august 2014 by John Chilton adding citation support
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5 #
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6 # updated august 8 2014 to fix bugs reported by Marius van den Beek
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7 # please cite the resource at
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8 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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9 # if you use this tool in your published work.
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10
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11 *Short Story*
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12
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13 This is an unusual Galaxy tool capable of generating new Galaxy tools.
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14 It works by exposing *unrestricted* and therefore extremely dangerous scripting
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15 to all designated administrators of the host Galaxy server, allowing them to
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16 run scripts in R, python, sh and perl over multiple selected input data sets,
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17 writing a single new data set as output.
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18
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19 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
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20
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20
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21 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
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20
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22
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23
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24 *Automated generation of new Galaxy tools for installation into any Galaxy*
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25
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26
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26 A test is generated using small sample test data inputs and parameter settings you supply.
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27 Once the test case outputs have been produced, they can be used to build a
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28 new Galaxy tool. The supplied script or executable is baked as a requirement
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29 into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
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30 Generated tools are installed via a tool shed by an administrator
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31 and work exactly like all other Galaxy tools for your users.
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32
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33 *More Detail*
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34
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35 To use the ToolFactory, you should have prepared a script to paste into a
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36 text box, or have a package in mind and a small test input example ready to select from your history
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37 to test your new script.
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38
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39 ```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
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40
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41 There is an example in each scripting language on the Tool Factory form. You
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42 can just cut and paste these to try it out - remember to select the right
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43 interpreter please. You'll also need to create a small test data set using
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44 the Galaxy history add new data tool.
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45
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46 If the script fails somehow, use the "redo" button on the tool output in
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47 your history to recreate the form complete with broken script. Fix the bug
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48 and execute again. Rinse, wash, repeat.
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49
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50 Once the script runs sucessfully, a new Galaxy tool that runs your script
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51 can be generated. Select the "generate" option and supply some help text and
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52 names. The new tool will be generated in the form of a new Galaxy datatype
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53 - toolshed.gz - as the name suggests, it's an archive ready to upload to a
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54 Galaxy ToolShed as a new tool repository.
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55
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56 Once it's in a ToolShed, it can be installed into any local Galaxy server
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57 from the server administrative interface.
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58
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59 Once the new tool is installed, local users can run it - each time, the script
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60 that was supplied when it was built will be executed with the input chosen
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61 from the user's history. In other words, the tools you generate with the
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62 ToolFactory run just like any other Galaxy tool,but run your script every time.
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63
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64 Tool factory tools are perfect for workflow components. One input, one output,
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65 no variables.
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66
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67 *To fully and safely exploit the awesome power* of this tool,
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68 Galaxy and the ToolShed, you should be a developer installing this
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69 tool on a private/personal/scratch local instance where you are an
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70 admin_user. Then, if you break it, you get to keep all the pieces see
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71 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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72
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73 ** Installation **
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74 This is a Galaxy tool. You can install it most conveniently using the
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75 administrative "Search and browse tool sheds" link. Find the Galaxy Main
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76 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
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77 repository. Open it and review the code and select the option to install it.
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78
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79 (
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80 If you can't get the tool that way, the xml and py files here need to be
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81 copied into a new tools
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82 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
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83 pointing to the xml
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84 file - something like::
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85
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86 <section name="Tool building tools" id="toolbuilders">
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87 <tool file="toolfactory/rgToolFactory.xml"/>
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88 </section>
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89
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90 If not already there (I just added it to datatypes_conf.xml.sample),
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91 please add:
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92 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
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93 mimetype="multipart/x-gzip" subclass="True" />
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94 to your local data_types_conf.xml.
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95 )
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96
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97 * Restricted execution *
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98 The tool factory tool itself will then be usable ONLY by admin users -
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99 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
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100 admin_users can run this tool** Think about it for a moment. If allowed to
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101 run any arbitrary script on your Galaxy server, the only thing that would
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102 impede a miscreant bent on destroying all your Galaxy data would probably
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103 be lack of appropriate technical skills.
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104
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105 *What it does* This is a tool factory for simple scripts in python, R and
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106 perl currently. Functional tests are automatically generated. How cool is that.
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107
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108 LIMITED to simple scripts that read one input from the history. Optionally can
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109 write one new history dataset, and optionally collect any number of outputs
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110 into links on an autogenerated HTML index page for the user to navigate -
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111 useful if the script writes images and output files - pdf outputs are shown
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112 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
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113 imagemagik need to be available.
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114
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115 Generated tools can be edited and enhanced like any Galaxy tool, so start
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116 small and build up since a generated script gets you a serious leg up to a
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117 more complex one.
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118
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119 *What you do* You paste and run your script, you fix the syntax errors and
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120 eventually it runs. You can use the redo button and edit the script before
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121 trying to rerun it as you debug - it works pretty well.
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122
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123 Once the script works on some test data, you can generate a toolshed compatible
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124 gzip file containing your script ready to run as an ordinary Galaxy tool in
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125 a repository on your local toolshed. That means safe and largely automated
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126 installation in any production Galaxy configured to use your toolshed.
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127
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128 *Generated tool Security* Once you install a generated tool, it's just
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129 another tool - assuming the script is safe. They just run normally and their
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130 user cannot do anything unusually insecure but please, practice safe toolshed.
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131 Read the fucking code before you install any tool. Especially this one -
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132 it is really scary.
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133
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134 If you opt for an HTML output, you get all the script outputs arranged
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135 as a single Html history item - all output files are linked, thumbnails for
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136 all the pdfs. Ugly but really inexpensive.
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137
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138 Patches and suggestions welcome as bitbucket issues please?
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139
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140 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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141
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142 all rights reserved
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143 Licensed under the LGPL if you want to improve it, feel free
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144 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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145
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146
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147 **Attribution**
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148 Creating re-usable tools from scripts: The Galaxy Tool Factory
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149 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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150 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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151
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152 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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153
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154 **Licensing**
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155 Copyright Ross Lazarus 2010
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156 ross lazarus at g mail period com
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157
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158 All rights reserved.
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159
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160 Licensed under the LGPL
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161
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162 **Obligatory screenshot**
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163
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164 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
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165
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