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42
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1 Note as at August 8 2020
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2
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3
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4 *WARNING before you start*
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5
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6 Install this tool on a private Galaxy ONLY
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7 Please NEVER on a public or production instance
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8
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9 Please cite the resource at
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10 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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11 if you use this tool in your published work.
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12
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13 **Short Story**
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14
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15 This is an unusual Galaxy tool capable of generating new Galaxy tools.
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16 It works by exposing *unrestricted* and therefore extremely dangerous scripting
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17 to all designated administrators of the host Galaxy server, allowing them to
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18 run scripts in R, python, sh and perl over multiple selected input data sets,
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19 writing a single new data set as output.
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20
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21 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
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22
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23 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
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24
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25 **Automated generation of new Galaxy tools for installation into any Galaxy**
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26
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27 A test is generated using small sample test data inputs and parameter settings you supply.
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28 Once the test case outputs have been produced, they can be used to build a
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29 new Galaxy tool. The supplied script or executable is baked as a requirement
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30 into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
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31 Generated tools are installed via a tool shed by an administrator
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32 and work exactly like all other Galaxy tools for your users.
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33
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34 **More Detail**
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35
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36 To use the ToolFactory, you should have prepared a script to paste into a
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37 text box, or have a package in mind and a small test input example ready to select from your history
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38 to test your new script.
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39
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40 ```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me
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41
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42 There is an example in each scripting language on the Tool Factory form. You
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43 can just cut and paste these to try it out - remember to select the right
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44 interpreter please. You'll also need to create a small test data set using
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45 the Galaxy history add new data tool.
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46
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47 If the script fails somehow, use the "redo" button on the tool output in
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48 your history to recreate the form complete with broken script. Fix the bug
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49 and execute again. Rinse, wash, repeat.
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50
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51 Once the script runs sucessfully, a new Galaxy tool that runs your script
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52 can be generated. Select the "generate" option and supply some help text and
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53 names. The new tool will be generated in the form of a new Galaxy datatype
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54 *tgz* - as the name suggests, it's an archive ready to upload to a
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55 Galaxy ToolShed as a new tool repository.
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56
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57
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58 Once it's in a ToolShed, it can be installed into any local Galaxy server
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59 from the server administrative interface.
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60
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61 Once the new tool is installed, local users can run it - each time, the script
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62 that was supplied when it was built will be executed with the input chosen
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63 from the user's history. In other words, the tools you generate with the
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64 ToolFactory run just like any other Galaxy tool,but run your script every time.
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65
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66 Tool factory tools are perfect for workflow components. One input, one output,
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67 no variables.
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68
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69 *To fully and safely exploit the awesome power* of this tool,
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70 Galaxy and the ToolShed, you should be a developer installing this
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71 tool on a private/personal/scratch local instance where you are an
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72 admin_user. Then, if you break it, you get to keep all the pieces see
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73 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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74
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75 **Installation**
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76 This is a Galaxy tool. You can install it most conveniently using the
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77 administrative "Search and browse tool sheds" link. Find the Galaxy Main
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78 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
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79 repository. Open it and review the code and select the option to install it.
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80
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81 If you can't get the tool that way, the xml and py files here need to be
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82 copied into a new tools
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83 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
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84 pointing to the xml
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85 file - something like::
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86
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87 <section name="Tool building tools" id="toolbuilders">
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88 <tool file="toolfactory/rgToolFactory.xml"/>
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89 </section>
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90
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91 If not already there,
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92 please add:
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93 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
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94 mimetype="multipart/x-gzip" subclass="True" />
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95 to your local data_types_conf.xml.
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96
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97
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98 **Restricted execution**
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99
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100 The tool factory tool itself will then be usable ONLY by admin users -
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101 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
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102 admin_users can run this tool** Think about it for a moment. If allowed to
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103 run any arbitrary script on your Galaxy server, the only thing that would
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104 impede a miscreant bent on destroying all your Galaxy data would probably
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105 be lack of appropriate technical skills.
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106
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107 **What it does**
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108
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109 This is a tool factory for simple scripts in python, R and
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110 perl currently. Functional tests are automatically generated.
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111
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112 LIMITED to simple scripts that read one input from the history. Optionally can
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113 write one new history dataset, and optionally collect any number of outputs
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114 into links on an autogenerated HTML index page for the user to navigate -
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115 useful if the script writes images and output files - pdf outputs are shown
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116 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
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117 imagemagik need to be available.
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118
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119 Generated tools can be edited and enhanced like any Galaxy tool, so start
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120 small and build up since a generated script gets you a serious leg up to a
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121 more complex one.
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122
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123 **What you do**
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124
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125 You paste and run your script, you fix the syntax errors and
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126 eventually it runs. You can use the redo button and edit the script before
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127 trying to rerun it as you debug - it works pretty well.
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128
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129 Once the script works on some test data, you can generate a toolshed compatible
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130 gzip file containing your script ready to run as an ordinary Galaxy tool in
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131 a repository on your local toolshed. That means safe and largely automated
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132 installation in any production Galaxy configured to use your toolshed.
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133
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134 **Generated tool Security**
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135
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136 Once you install a generated tool, it's just
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137 another tool - assuming the script is safe. They just run normally and their
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138 user cannot do anything unusually insecure but please, practice safe toolshed.
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139 Read the code before you install any tool. Especially this one - it is really scary.
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140
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141 **Send Code**
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142
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143 Patches and suggestions welcome as bitbucket issues please?
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144
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145 **Attribution**
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146
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147 Creating re-usable tools from scripts: The Galaxy Tool Factory
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148 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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149 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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150
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151 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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152
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153 **Licensing**
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154
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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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