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date Fri, 30 Apr 2021 02:10:32 +0000
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43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again
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1 *WARNING before you start*
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2
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3 Install this tool on a private Galaxy ONLY
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4 Please NEVER on a public or production instance
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5
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6 Updated august 2014 by John Chilton adding citation support
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7
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8 Updated august 8 2014 to fix bugs reported by Marius van den Beek
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9
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10 Please cite the resource at
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11 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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12 if you use this tool in your published work.
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13
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14 **Short Story**
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15
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16 This is an unusual Galaxy tool capable of generating new Galaxy tools.
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17 It works by exposing *unrestricted* and therefore extremely dangerous scripting
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18 to all designated administrators of the host Galaxy server, allowing them to
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19 run scripts in R, python, sh and perl over multiple selected input data sets,
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20 writing a single new data set as output.
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21
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22 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
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23
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24 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
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25
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26
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27 **Automated generation of new Galaxy tools for installation into any Galaxy**
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28
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29 A test is generated using small sample test data inputs and parameter settings you supply.
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30 Once the test case outputs have been produced, they can be used to build a
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31 new Galaxy tool. The supplied script or executable is baked as a requirement
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32 into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
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33 Generated tools are installed via a tool shed by an administrator
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34 and work exactly like all other Galaxy tools for your users.
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35
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36 **More Detail**
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37
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38 To use the ToolFactory, you should have prepared a script to paste into a
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39 text box, or have a package in mind and a small test input example ready to select from your history
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40 to test your new script.
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41
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42 ```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
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43
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44 There is an example in each scripting language on the Tool Factory form. You
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45 can just cut and paste these to try it out - remember to select the right
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46 interpreter please. You'll also need to create a small test data set using
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47 the Galaxy history add new data tool.
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48
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49 If the script fails somehow, use the "redo" button on the tool output in
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50 your history to recreate the form complete with broken script. Fix the bug
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51 and execute again. Rinse, wash, repeat.
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52
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53 Once the script runs sucessfully, a new Galaxy tool that runs your script
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54 can be generated. Select the "generate" option and supply some help text and
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55 names. The new tool will be generated in the form of a new Galaxy datatype
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56 *toolshed.gz* - as the name suggests, it's an archive ready to upload to a
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57 Galaxy ToolShed as a new tool repository.
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58
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59 Once it's in a ToolShed, it can be installed into any local Galaxy server
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60 from the server administrative interface.
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61
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62 Once the new tool is installed, local users can run it - each time, the script
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63 that was supplied when it was built will be executed with the input chosen
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64 from the user's history. In other words, the tools you generate with the
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65 ToolFactory run just like any other Galaxy tool,but run your script every time.
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66
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67 Tool factory tools are perfect for workflow components. One input, one output,
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68 no variables.
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69
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70 *To fully and safely exploit the awesome power* of this tool,
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71 Galaxy and the ToolShed, you should be a developer installing this
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72 tool on a private/personal/scratch local instance where you are an
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73 admin_user. Then, if you break it, you get to keep all the pieces see
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74 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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75
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76 **Installation**
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77 This is a Galaxy tool. You can install it most conveniently using the
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78 administrative "Search and browse tool sheds" link. Find the Galaxy Main
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79 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
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80 repository. Open it and review the code and select the option to install it.
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81
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82 If you can't get the tool that way, the xml and py files here need to be
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83 copied into a new tools
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84 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
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85 pointing to the xml
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86 file - something like::
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87
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88 <section name="Tool building tools" id="toolbuilders">
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89 <tool file="toolfactory/rgToolFactory.xml"/>
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90 </section>
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91
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92 If not already there,
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93 please add:
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94 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
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95 mimetype="multipart/x-gzip" subclass="True" />
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96 to your local data_types_conf.xml.
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97
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98
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99 **Restricted execution**
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100
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101 The tool factory tool itself will then be usable ONLY by admin users -
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102 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
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103 admin_users can run this tool** Think about it for a moment. If allowed to
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104 run any arbitrary script on your Galaxy server, the only thing that would
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105 impede a miscreant bent on destroying all your Galaxy data would probably
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106 be lack of appropriate technical skills.
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107
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108 **What it does**
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109
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110 This is a tool factory for simple scripts in python, R and
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111 perl currently. Functional tests are automatically generated. How cool is that.
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112
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113 LIMITED to simple scripts that read one input from the history. Optionally can
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114 write one new history dataset, and optionally collect any number of outputs
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115 into links on an autogenerated HTML index page for the user to navigate -
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116 useful if the script writes images and output files - pdf outputs are shown
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117 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
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118 imagemagik need to be available.
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119
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120 Generated tools can be edited and enhanced like any Galaxy tool, so start
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121 small and build up since a generated script gets you a serious leg up to a
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122 more complex one.
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123
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124 **What you do**
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125
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126 You paste and run your script, you fix the syntax errors and
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127 eventually it runs. You can use the redo button and edit the script before
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128 trying to rerun it as you debug - it works pretty well.
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129
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130 Once the script works on some test data, you can generate a toolshed compatible
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131 gzip file containing your script ready to run as an ordinary Galaxy tool in
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132 a repository on your local toolshed. That means safe and largely automated
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133 installation in any production Galaxy configured to use your toolshed.
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134
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135 **Generated tool Security**
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136
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137 Once you install a generated tool, it's just
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138 another tool - assuming the script is safe. They just run normally and their
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139 user cannot do anything unusually insecure but please, practice safe toolshed.
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140 Read the code before you install any tool. Especially this one - it is really scary.
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141
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142 **Send Code**
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143
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144 Patches and suggestions welcome as bitbucket issues please?
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145
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146 **Attribution**
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147
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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**
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again
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155
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again
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156 Copyright Ross Lazarus 2010
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157 ross lazarus at g mail period com
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158
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159 All rights reserved.
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again
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160
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161 Licensed under the LGPL
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162
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163 **Obligatory screenshot**
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164
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165 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
43edf22e8cbc Toolshed seems cranky on very old metadata. Trying a new repo. Again
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166