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30
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1 toolfactory_2
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2 =============
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3
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4 This is an upgrade to the tool factory but with added parameters
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5 (optionally editable in the generated tool form - otherwise fixed) and
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6 multiple input files.
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7
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8 Specify any number of parameters - well at
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9 least up to the limit of your patience with repeat groups.
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10
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11 Parameter values supplied at tool generation time are defaults and
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12 can be optionally editable by the user - names cannot be changed once
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13 a tool has been generated.
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14
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15 If not editable, they act as hidden parameters passed to the script
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16 and are not editable on the tool form.
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17
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18 Note! There will be Galaxy default sanitization for all
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19 user input parameters which your script may need to dance around.
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20
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21 Any number of input files can be passed to your script, but of course it
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22 has to deal with them. Both path and metadata name are supplied either in the environment
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23 (bash/sh) or as command line parameters (python,perl,rscript) that need to be parsed and
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24 dealt with in the script. This is complicated by the common use case of needing file names
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25 for (eg) column headers, as well as paths. Try the examples are show on the tool factory
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26 form to see how Galaxy file and user supplied parameter values can be recovered in each
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27 of the 4 scripting environments supported.
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28
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29 Best way to deal with multiple outputs is to let the tool factory generate an HTML
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30 page for your users. It automagically lays out pdf images as thumbnail galleries
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31 and can have separate results sections gathering all similarly prefixed files, such as
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32 a Foo section taking text and results from text (foo_whatever.log) and
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33 artifacts (eg foo_MDS_plot.pdf) file names. All artifacts are linked for download.
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34 A copy of the actual script is provided for provenance - be warned, it exposes
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35 real file paths.
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36
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37 **WARNING before you start**
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38
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39 Install this tool on a private Galaxy ONLY
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40 Please NEVER on a public or production instance
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41 Please cite the resource at
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42 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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43 if you use this tool in your published work.
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44
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45
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46 *Short Story*
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47
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48 This is an unusual Galaxy tool capable of generating new Galaxy tools.
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49 It works by exposing *unrestricted* and therefore extremely dangerous scripting
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50 to all designated administrators of the host Galaxy server, allowing them to
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51 run scripts in R, python, sh and perl over multiple selected input data sets,
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52 writing a single new data set as output.
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53
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54 *Differences between TF2 and the original Tool Factory*
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55
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56 1. TF2 (this one) allows any number of either fixed or user-editable parameters to be defined
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57 for the new tool. If these are editable, the user can change them but otherwise, they are passed
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58 as fixed and invisible parameters for each execution. Obviously, there are substantial security
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59 implications with editable parameters, but these are always sanitized by Galaxy's inbuilt
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60 parameter sanitization so you may need to "unsanitize" characters - eg translate all "__lt__"
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61 into "<" for certain parameters where that is needed. Please practise safe toolshed.
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62
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63 2. Any number of (the same datatype) of input files may be defined.
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64
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65 These changes substantially complicate the way your supplied script is supplied with
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66 all the new and variable parameters. Examples in each scripting language are shown
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67 in the tool help
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68
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69 *Automated outputs in named sections*
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70
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71 If your script writes to the current directory path, arbitrary mix of (eg)
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72 pdfs, tabular analysis results and run logs,the tool factory can optionally
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73 auto-generate a linked Html page with separate sections showing a thumbnail
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74 grid for all pdfs and the log text, grouping all artifacts sharing a file
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75 name and log name prefix.if "foo.log" is emitted then *all* other outputs matching foo_* will
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76 all be grouped together - eg
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77 - foo_baz.pdf
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78 - foo_bar.pdf and
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79 - foo_zot.xls
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80
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81 would all be displayed and linked in the same section with foo.log's contents to form the "Foo" section of the Html page.
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82 Sections appear in alphabetic order and there are no limits on the number of files or sections.
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83
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84 *Automated generation of new Galaxy tools for installation into any Galaxy*
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85
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86 Once a script is working correctly, this tool optionally generates a
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87 new Galaxy tool, effectively freezing the supplied script into a new,
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88 ordinary Galaxy tool that runs it over one or more input files selected by
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89 the user. Generated tools are installed via a tool shed by an administrator
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90 and work exactly like all other Galaxy tools for your users.
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91
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92 If you use the Html output option, please ensure that sanitize_all_html is
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93 set to False and uncommented in universe_wsgi.ini - it should show
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94
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95 By default, all tool output served as 'text/html' will be sanitized
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96 Change ```sanitize_all_html = False```
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97
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98 This opens potential security risks and may not be acceptable for public
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99 sites where the lack of stylesheets may make Html pages damage onlookers'
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100 eyeballs but should still be correct.
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101
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102 *More Detail*
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103
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104 To use the ToolFactory, you should have prepared a script to paste into a
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105 text box, and a small test input example ready to select from your history
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106 to test your new script.
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107
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108 There is an example in each scripting language on the Tool Factory form. You
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109 can just cut and paste these to try it out - remember to select the right
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110 interpreter please. You'll also need to create a small test data set using
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111 the Galaxy history add new data tool.
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112
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113 If the script fails somehow, use the "redo" button on the tool output in
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114 your history to recreate the form complete with broken script. Fix the bug
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115 and execute again. Rinse, wash, repeat.
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116
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117 Once the script runs sucessfully, a new Galaxy tool that runs your script
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118 can be generated. Select the "generate" option and supply some help text and
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119 names. The new tool will be generated in the form of a new Galaxy datatype
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120 - toolshed.gz - as the name suggests, it's an archive ready to upload to a
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121 Galaxy ToolShed as a new tool repository.
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122
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123 Once it's in a ToolShed, it can be installed into any local Galaxy server
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124 from the server administrative interface.
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125
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126 Once the new tool is installed, local users can run it - each time, the script
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127 that was supplied when it was built will be executed with the input chosen
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128 from the user's history. In other words, the tools you generate with the
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129 ToolFactory run just like any other Galaxy tool,but run your script every time.
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130
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131 Tool factory tools are perfect for workflow components. One input, one output,
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132 no variables.
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133
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134 *To fully and safely exploit the awesome power* of this tool,
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135 Galaxy and the ToolShed, you should be a developer installing this
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136 tool on a private/personal/scratch local instance where you are an
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137 admin_user. Then, if you break it, you get to keep all the pieces see
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138 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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139
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140 ** Installation **
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141 This is a Galaxy tool. You can install it most conveniently using the
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142 administrative "Search and browse tool sheds" link. Find the Galaxy Main
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143 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
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144 repository. Open it and review the code and select the option to install it.
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145
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146
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147 If you can't get the tool that way, the xml and py files here need to be
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148 copied into a new tools subdirectory such as tools/toolfactory
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149 Your tool_conf.xml needs a new entry pointing to the xml \file - something like
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150 ```
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151 <section name="Tool building tools" id="toolbuilders">
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152 <tool file="toolfactory/rgToolFactory.xml"/>
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153 </section>
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154 ```
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155 If not already there (I just added it to datatypes_conf.xml.sample),
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156 please add:
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157
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158 ```
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159 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
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160 mimetype="multipart/x-gzip" subclass="True" />
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161 ```
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162 to your local data_types_conf.xml.
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163
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164
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165 Of course, R, python, perl etc are needed on your path if you want to test
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166 scripts using those interpreters. Adding new ones to this tool code should
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167 be easy enough. Please make suggestions as bitbucket issues and code. The
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168 HTML file code automatically shrinks R's bloated pdfs, and depends on
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169 ghostscript. The thumbnails require imagemagick .
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170
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171 * Restricted execution *
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172 The tool factory tool itself will then be usable ONLY by admin users -
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173 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
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174 admin_users can run this tool** Think about it for a moment. If allowed to
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175 run any arbitrary script on your Galaxy server, the only thing that would
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176 impede a miscreant bent on destroying all your Galaxy data would probably
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177 be lack of appropriate technical skills.
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178
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179 *What it does* This is a tool factory for simple scripts in python, R and
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180 perl currently. Functional tests are automatically generated. How cool is that.
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181
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182 LIMITED to simple scripts that read one input from the history. Optionally can
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183 write one new history dataset, and optionally collect any number of outputs
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184 into links on an autogenerated HTML index page for the user to navigate -
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185 useful if the script writes images and output files - pdf outputs are shown
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186 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
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187 imagemagik need to be available.
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188
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189 Generated tools can be edited and enhanced like any Galaxy tool, so start
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190 small and build up since a generated script gets you a serious leg up to a
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191 more complex one.
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192
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193 *What you do* You paste and run your script, you fix the syntax errors and
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194 eventually it runs. You can use the redo button and edit the script before
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195 trying to rerun it as you debug - it works pretty well.
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196
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197 Once the script works on some test data, you can generate a toolshed compatible
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198 gzip file containing your script ready to run as an ordinary Galaxy tool in
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199 a repository on your local toolshed. That means safe and largely automated
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200 installation in any production Galaxy configured to use your toolshed.
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201
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202 *Generated tool Security* Once you install a generated tool, it's just
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203 another tool - assuming the script is safe. They just run normally and their
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204 user cannot do anything unusually insecure but please, practice safe toolshed.
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205 Read the fucking code before you install any tool. Especially this one -
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206 it is really scary.
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207
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208 If you opt for an HTML output, you get all the script outputs arranged
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209 as a single Html history item - all output files are linked, thumbnails for
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210 all the pdfs. Ugly but really inexpensive.
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211
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212 Patches and suggestions welcome as bitbucket issues please?
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213
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214 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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215
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216 all rights reserved
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217 Licensed under the LGPL if you want to improve it, feel free
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218 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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219
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220 Material for our more enthusiastic and voracious readers continues below -
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221 we salute you.
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222
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223 **Motivation** Simple transformation, filtering or reporting scripts get
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224 written, run and lost every day in most busy labs - even ours where Galaxy is
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225 in use. This 'dark script matter' is pervasive and generally not reproducible.
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226
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227 **Benefits** For our group, this allows Galaxy to fill that important dark
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228 script gap - all those "small" bioinformatics tasks. Once a user has a working
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229 R (or python or perl) script that does something Galaxy cannot currently do
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230 (eg transpose a tabular file) and takes parameters the way Galaxy supplies
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231 them (see example below), they:
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232
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233 1. Install the tool factory on a personal private instance
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234
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235 2. Upload a small test data set
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236
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237 3. Paste the script into the 'script' text box and iteratively run the
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238 insecure tool on test data until it works right - there is absolutely no
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239 reason to do this anywhere other than on a personal private instance.
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240
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241 4. Once it works right, set the 'Generate toolshed gzip' option and run
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242 it again.
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243
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244 5. A toolshed style gzip appears ready to upload and install like any other
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245 Toolshed entry.
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246
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247 6. Upload the new tool to the toolshed
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248
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249 7. Ask the local admin to check the new tool to confirm it's not evil and
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250 install it in the local production galaxy
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251
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252
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253
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254 **Parameter passing and file inputs**
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255
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256 Your script will receive up to 3 named parameters
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257 INPATHS is a comma separated list of input file paths
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258 INNAMES is a comma separated list of input file names in the same order
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259 OUTPATH is optional if a file is being generated, your script should write there
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260 Your script should open and write files in the provided working directory if you are using the Html
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261 automatic presentation option.
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262
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263 Python script command lines will have --INPATHS and --additional_arguments etc. to make it easy to use argparse
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264
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265 Rscript will need to use commandArgs(TRUE) - see the example below - additional arguments will
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266 appear as themselves - eg foo="bar" will mean that foo is defined as "bar" for the script.
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267
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268 Bash and sh will see any additional parameters on their command lines and the 3 named parameters
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269 in their environment magically - well, using env on the CL
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270 ```
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271 ***python***::
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272
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273 # argparse for 3 possible comma separated lists
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274 # additional parameters need to be parsed !
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275 # then echo parameters to the output file
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276 import sys
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277 import argparse
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278 argp=argparse.ArgumentParser()
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279 argp.add_argument('--INNAMES',default=None)
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280 argp.add_argument('--INPATHS',default=None)
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281 argp.add_argument('--OUTPATH',default=None)
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282 argp.add_argument('--additional_parameters',default=[],action="append")
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283 argp.add_argument('otherargs', nargs=argparse.REMAINDER)
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284 args = argp.parse_args()
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285 f= open(args.OUTPATH,'w')
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286 s = '### args=%s\n' % str(args)
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287 f.write(s)
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288 s = 'sys.argv=%s\n' % sys.argv
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289 f.write(s)
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290 f.close()
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291
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292
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293
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294 ***Rscript***::
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295
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296 # tool factory Rscript parser suggested by Forester
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297 # http://www.r-bloggers.com/including-arguments-in-r-cmd-batch-mode/
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298 # additional parameters will appear in the ls() below - they are available
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299 # to your script
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300 # echo parameters to the output file
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301 ourargs = commandArgs(TRUE)
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302 if(length(ourargs)==0){
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303 print("No arguments supplied.")
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304 }else{
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305 for(i in 1:length(ourargs)){
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306 eval(parse(text=ourargs[[i]]))
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307 }
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308 sink(OUTPATH)
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309 cat('INPATHS=',INPATHS,'\n')
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310 cat('INNAMES=',INNAMES,'\n')
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311 cat('OUTPATH=',OUTPATH,'\n')
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312 x=ls()
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313 cat('all objects=',x,'\n')
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314 sink()
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315 }
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316 sessionInfo()
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317 print.noquote(date())
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318
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319
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320 ***bash/sh***::
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321
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322 # tool factory sets up these environmental variables
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323 # this example writes those to the output file
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324 # additional params appear on command line
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325 if [ ! -f "$OUTPATH" ] ; then
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326 touch "$OUTPATH"
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327 fi
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328 echo "INPATHS=$INPATHS" >> "$OUTPATH"
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329 echo "INNAMES=$INNAMES" >> "$OUTPATH"
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330 echo "OUTPATH=$OUTPATH" >> "$OUTPATH"
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331 echo "CL=$@" >> "$OUTPATH"
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332
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333 ***perl***::
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334
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335 (my $INPATHS,my $INNAMES,my $OUTPATH ) = @ARGV;
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336 open(my $fh, '>', $OUTPATH) or die "Could not open file '$OUTPATH' $!";
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337 print $fh "INPATHS=$INPATHS\n INNAMES=$INNAMES\n OUTPATH=$OUTPATH\n";
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338 close $fh;
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339
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340 ```
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341
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342 Galaxy as an IDE for developing API scripts
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343 If you need to develop Galaxy API scripts and you like to live dangerously,
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344 please read on.
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345
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346 Galaxy as an IDE?
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347 Amazingly enough, blend-lib API scripts run perfectly well *inside*
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348 Galaxy when pasted into a Tool Factory form. No need to generate a new
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349 tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously,
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350 it is actually quite useable.
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351
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352 Why bother - what's wrong with Eclipse
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353 Nothing. But, compared with developing API scripts in the usual way outside
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354 Galaxy, you get persistence and other framework benefits plus at absolutely
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355 no extra charge, a ginormous security problem if you share the history or
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356 any outputs because they contain the api script with key so development
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357 servers only please!
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358
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359 Workflow
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360 Fire up the Tool Factory in Galaxy.
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361
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362 Leave the input box empty, set the interpreter to python, paste and run an
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363 api script - eg working example (substitute the url and key) below.
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364
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365 It took me a few iterations to develop the example below because I know
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366 almost nothing about the API. I started with very simple code from one of the
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367 samples and after each run, the (edited..) api script is conveniently recreated
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368 using the redo button on the history output item. So each successive version
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369 of the developing api script you run is persisted - ready to be edited and
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370 rerun easily. It is ''very'' handy to be able to add a line of code to the
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371 script and run it, then view the output to (eg) inspect dicts returned by
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372 API calls to help move progressively deeper iteratively.
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373
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374 Give the below a whirl on a private clone (install the tool factory from
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375 the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.
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376
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377 Eg tool factory api script
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378 ```
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379 import sys
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380 from blend.galaxy import GalaxyInstance
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381 ourGal = 'http://x.x.x.x:xxxx'
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382 ourKey = 'xxx'
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383 gi = GalaxyInstance(ourGal, key=ourKey)
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384 libs = gi.libraries.get_libraries()
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385 res = []
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386 # libs looks like
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387 # u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id':
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388 u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
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389 for lib in libs:
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390 res.append('%s:\n' % lib['name'])
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391 res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
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392 outf=open(sys.argv[2],'w')
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393 outf.write('\n'.join(res))
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394 outf.close()
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395 ```
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396
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397 **Attribution**
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398 Creating re-usable tools from scripts: The Galaxy Tool Factory
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399 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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400 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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401
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402 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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403
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404 **Licensing**
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405 Copyright Ross Lazarus 2010
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406 ross lazarus at g mail period com
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407
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408 All rights reserved.
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409
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410 Licensed under the LGPL
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411
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412 **screenshot**
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413
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414 
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415
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416
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417 ```
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418
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