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annotate fubar-galaxytoolfactory-58871556de57/README.txt @ 6:cb4937b0c21d draft

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This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
author fubar
date Sun, 24 Feb 2013 17:15:29 -0500
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cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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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
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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5 Please cite:
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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6 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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7 if you use this tool in your published work.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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8
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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9 *Short Story*
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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10
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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11 This is an unusual Galaxy tool that exposes unrestricted and therefore extremely dangerous
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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12 scripting to designated administrative users of a Galaxy server, allowing them to run scripts
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13 in R, python, sh and perl over a single input data set, writing a single new data set as output.
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14
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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15 In addition, this tool optionally generates very simple new Galaxy tools, that effectively
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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16 freeze the supplied script into a new, ordinary Galaxy tool that runs it over a single input file,
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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17 working just like any other Galaxy tool for your users.
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18
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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19 To use the ToolFactory, you should have prepared a script to paste into a text box,
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20 and a small test input example ready to select from your history to test your new script.
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21 There is an example in each scripting language on the Tool Factory form. You can just
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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22 cut and paste these to try it out - remember to select the right interpreter please. You'll
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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23 also need to create a small test data set using the Galaxy history add new data tool.
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24
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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25 If the script fails somehow, use the "redo" button on the tool output in your history to
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26 recreate the form complete with broken script. Fix the bug and execute again. Rinse, wash, repeat.
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27
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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28 Once the script runs sucessfully, a new Galaxy tool that runs your script can be generated.
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29 Select the "generate" option and supply some help text and names. The new tool will be
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30 generated in the form of a new Galaxy datatype - toolshed.gz - as the name suggests,
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31 it's an archive ready to upload to a Galaxy ToolShed as a new tool repository.
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32
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33 Once it's in a ToolShed, it can be installed into any local Galaxy server from
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34 the server administrative interface.
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35
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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36 Once the new tool is installed, local users can run it - each time, the script that was supplied
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37 when it was built will be executed with the input chosen from the user's history. In other words,
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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38 the tools you generate with the ToolFactory run just like any other Galaxy tool,
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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39 but run your script every time.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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40
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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41 Tool factory tools are perfect for workflow components. One input, one output, no variables.
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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42
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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43 *Reasons to read further*
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44
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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45 If you use Galaxy to support your research;
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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46
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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47 You and fellow users are sometimes forced to take data out of Galaxy, process it with ugly
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48 little perl/awk/sed/R... scripts and put it back;
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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49
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50 You do this when you can't do some transformation in Galaxy (the 90/10 rule);
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51
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52 You don't have enough developer resources for wrapping dozens of even relatively simple tools;
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53
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54 Your research and your institution would be far better off if those feral scripts were all tucked
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55 safely in your local toolshed and Galaxy histories.
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56
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57 *The good news* If it can be trivially scripted, it can be running safely in your
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58 local Galaxy via your own local toolshed in a few minutes - with functional tests.
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59
cb4937b0c21d This fixes a problem reported by Carlos with perl scripts - now use CDATA segments to protect that horrible syntax from Cheetah - seems to work properly now.
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60
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61 *Value proposition* The ToolFactory allows Galaxy to efficiently take over most of your lab's
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62 dark script matter, making it reproducible in Galaxy and shareable through the ToolShed.
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63
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64 That's what this tool does. You paste a simple script and the tool returns
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65 a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
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66 Scripts can be wrapped and online literally within minutes.
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67
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68 *To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
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69 you should be a developer installing this tool on a private/personal/scratch local instance where you
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70 are an admin_user. Then, if you break it, you get to keep all the pieces
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71 see 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 administrative "Search and browse tool sheds" link.
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75 Find the Galaxy Test toolshed (not main) and search for the toolfactory repository.
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76 Open it and review the code and select the option to install it.
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77
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78 If you can't get the tool that way, the xml and py files here need to be copied into a new tools
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79 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry pointing to the xml
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80 file - something like::
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81
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82 <section name="Tool building tools" id="toolbuilders">
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83 <tool file="toolfactory/rgToolFactory.xml"/>
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84 </section>
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85
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86 If not already there (I just added it to datatypes_conf.xml.sample), please add:
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87 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
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88 to your local data_types_conf.xml.
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89
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90 Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini
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91
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92 You'll have to restart the server for the new tool to be available.
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93
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94 Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
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95 Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
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96 The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
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97
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98 * Restricted execution *
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99 The new tool factory tool will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini
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100 **Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any
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101 arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
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102 Galaxy data would probably be lack of appropriate technical skills.
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103
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104 *What it does* This is a tool factory for simple scripts in python, R and perl currently.
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105 Functional tests are automatically generated. How cool is that.
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106
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107 LIMITED to simple scripts that read one input from the history.
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108 Optionally can write one new history dataset,
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109 and optionally collect any number of outputs into links on an autogenerated HTML
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110 index page for the user to navigate - useful if the script writes images and output files - pdf outputs
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111 are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to
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112 be avaailable.
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113
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114 Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since
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115 a generated script gets you a serious leg up to a more complex one.
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116
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117 *What you do* You paste and run your script
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118 you fix the syntax errors and eventually it runs
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119 You can use the redo button and edit the script before
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120 trying to rerun it as you debug - it works pretty well.
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121
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122 Once the script works on some test data, you can
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123 generate a toolshed compatible gzip file
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124 containing your script ready to run as an ordinary Galaxy tool in a
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125 repository on your local toolshed. That means safe and largely automated installation in any
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126 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 user cannot do anything unusually insecure
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130 but please, practice safe toolshed.
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131 Read the fucking code before you install any tool.
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132 Especially this one - 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 all the pdfs.
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136 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 long route to June 2012 product
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141 derived from an integrated script model
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142 called rgBaseScriptWrapper.py
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143 Note to the unwary:
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144 This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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145 There is nothing stopping a malicious user doing whatever they choose
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146 Extremely dangerous!!
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147 Totally insecure. So, trusted users only
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148
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149
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150
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151
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152 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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153
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154 all rights reserved
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155 Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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156
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157 Material for our more enthusiastic and voracious readers continues below - we salute you.
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158
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159 **Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
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160 - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
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161
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162 **Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
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163 tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a
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164 tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
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165
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166 1. Install the tool factory on a personal private instance
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167
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168 2. Upload a small test data set
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169
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170 3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right -
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171 there is absolutely no reason to do this anywhere other than on a personal private instance.
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172
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173 4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
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174
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175 5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
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176
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177 6. Upload the new tool to the toolshed
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178
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179 7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy
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180
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181 **Simple examples on the tool form**
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182
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183 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
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184 does something (transpose in this case) and writes the results to a new tabular file::
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185
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186 # transpose a tabular input file and write as a tabular output file
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187 ourargs = commandArgs(TRUE)
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188 inf = ourargs[1]
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189 outf = ourargs[2]
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190 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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191 outp = t(inp)
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192 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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193
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194 Calculate a multiple test adjusted p value from a column of p values - for this script to be useful,
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195 it needs the right column for the input to be specified in the code for the
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196 given input file type(s) specified when the tool is generated ::
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197
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198 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
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199 column = 1 # adjust if necessary for some other kind of input
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200 fdrmeth = 'BH'
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201 ourargs = commandArgs(TRUE)
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202 inf = ourargs[1]
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203 outf = ourargs[2]
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204 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
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205 p = inp[,column]
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206 q = p.adjust(p,method=fdrmeth)
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207 newval = paste(fdrmeth,'p-value',sep='_')
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208 q = data.frame(q)
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209 names(q) = newval
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210 outp = cbind(inp,newval=q)
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211 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
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212
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213
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214
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215 Another Rscript example without any input file - generates a random heatmap pdf - you must make sure the option to create an HTML output file is
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216 turned on for this to work. The heatmap will be presented as a thumbnail linked to the pdf in the resulting HTML page::
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217
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218 # note this script takes NO input or output because it generates random data
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219 foo = data.frame(a=runif(100),b=runif(100),c=runif(100),d=runif(100),e=runif(100),f=runif(100))
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220 bar = as.matrix(foo)
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221 pdf( "heattest.pdf" )
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222 heatmap(bar,main='Random Heatmap')
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223 dev.off()
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224
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225 A Python example that reverses each row of a tabular file. You'll need to remove the leading spaces for this to work if cut
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226 and pasted into the script box. Note that you can already do this in Galaxy by setting up the cut columns tool with the
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227 correct number of columns in reverse order,but this script will work for any number of columns so is completely generic::
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228
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229 # reverse order of columns in a tabular file
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230 import sys
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231 inp = sys.argv[1]
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232 outp = sys.argv[2]
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233 i = open(inp,'r')
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234 o = open(outp,'w')
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235 for row in i:
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236 rs = row.rstrip().split('\t')
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237 rs.reverse()
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238 o.write('\t'.join(rs))
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239 o.write('\n')
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240 i.close()
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241 o.close()
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242
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243
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244 Galaxy as an IDE for developing API scripts
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245 If you need to develop Galaxy API scripts and you like to live dangerously, please read on.
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246
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247 Galaxy as an IDE?
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248 Amazingly enough, blend-lib API scripts run perfectly well *inside* Galaxy when pasted into a Tool Factory form. No need to generate a new tool. Galaxy+Tool_Factory = IDE I think we need a new t-shirt. Seriously, it is actually quite useable.
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249
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250 Why bother - what's wrong with Eclipse
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251 Nothing. But, compared with developing API scripts in the usual way outside Galaxy, you get persistence and other framework benefits plus at absolutely no extra charge, a ginormous security problem if you share the history or any outputs because they contain the api script with key so development servers only please!
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252
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253 Workflow
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254 Fire up the Tool Factory in Galaxy.
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255
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256 Leave the input box empty, set the interpreter to python, paste and run an api script - eg working example (substitute the url and key) below.
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257
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258 It took me a few iterations to develop the example below because I know almost nothing about the API. I started with very simple code from one of the samples and after each run, the (edited..) api script is conveniently recreated using the redo button on the history output item. So each successive version of the developing api script you run is persisted - ready to be edited and rerun easily. It is ''very'' handy to be able to add a line of code to the script and run it, then view the output to (eg) inspect dicts returned by API calls to help move progressively deeper iteratively.
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259
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260 Give the below a whirl on a private clone (install the tool factory from the main toolshed) and try adding complexity with few rerun/edit/rerun cycles.
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261
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262 Eg tool factory api script
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263 import sys
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264 from blend.galaxy import GalaxyInstance
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265 ourGal = 'http://x.x.x.x:xxxx'
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266 ourKey = 'xxx'
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267 gi = GalaxyInstance(ourGal, key=ourKey)
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268 libs = gi.libraries.get_libraries()
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269 res = []
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270 # libs looks like
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271 # u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
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272 for lib in libs:
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273 res.append('%s:\n' % lib['name'])
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274 res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
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275 outf=open(sys.argv[2],'w')
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276 outf.write('\n'.join(res))
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277 outf.close()
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278
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279 **Attribution**
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280 Creating re-usable tools from scripts: The Galaxy Tool Factory
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281 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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282 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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283
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284 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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285
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286 **Licensing**
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287 Copyright Ross Lazarus 2010
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288 ross lazarus at g mail period com
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289
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290 All rights reserved.
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291
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292 Licensed under the LGPL
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293
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294 **Obligatory screenshot**
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295
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296 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
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297