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Citations added (thanks John!) and a few more output formats for Alistair Chilcott
author fubar
date Thu, 28 Aug 2014 02:33:05 -0400
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1 # WARNING before you start
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2 # Install this tool on a private Galaxy ONLY
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3 # Please NEVER on a public or production instance
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4 # updated august 8 2014 to fix bugs reported by Marius van den Beek
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5 Please cite:
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6 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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7 if you use this tool in your published work.
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8
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9 *Short Story*
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10
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11 This is an unusual Galaxy tool that exposes unrestricted and therefore extremely dangerous
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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
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15 In addition, this tool optionally generates very simple new Galaxy tools, that effectively
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16 freeze the supplied script into a new, ordinary Galaxy tool that runs it over a single input file,
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17 working just like any other Galaxy tool for your users.
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18
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19 If you use the Html output option, please ensure that sanitize_all_html is set to False and
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20 uncommented in universe_wsgi.ini - it should show:
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21
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22 # By default, all tool output served as 'text/html' will be sanitized
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23 sanitize_all_html = False
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24
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25
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26 *More Detail*
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27
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28 To use the ToolFactory, you should have prepared a script to paste into a text box,
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29 and a small test input example ready to select from your history to test your new script.
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30 There is an example in each scripting language on the Tool Factory form. You can just
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31 cut and paste these to try it out - remember to select the right interpreter please. You'll
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32 also need to create a small test data set using the Galaxy history add new data tool.
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33
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34 If the script fails somehow, use the "redo" button on the tool output in your history to
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35 recreate the form complete with broken script. Fix the bug and execute again. Rinse, wash, repeat.
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36
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37 Once the script runs sucessfully, a new Galaxy tool that runs your script can be generated.
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38 Select the "generate" option and supply some help text and names. The new tool will be
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39 generated in the form of a new Galaxy datatype - toolshed.gz - as the name suggests,
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40 it's an archive ready to upload to a Galaxy ToolShed as a new tool repository.
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41
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42 Once it's in a ToolShed, it can be installed into any local Galaxy server from
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43 the server administrative interface.
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44
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45 Once the new tool is installed, local users can run it - each time, the script that was supplied
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46 when it was built will be executed with the input chosen from the user's history. In other words,
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47 the tools you generate with the ToolFactory run just like any other Galaxy tool,
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48 but run your script every time.
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49
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50 Tool factory tools are perfect for workflow components. One input, one output, no variables.
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51
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52 *To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
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53 you should be a developer installing this tool on a private/personal/scratch local instance where you
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54 are an admin_user. Then, if you break it, you get to keep all the pieces
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55 see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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56
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57 ** Installation **
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58 This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link.
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59 Find the Galaxy Main toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory repository.
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60 Open it and review the code and select the option to install it.
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61
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62 (
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63 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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64 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry pointing to the xml
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65 file - something like::
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66
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67 <section name="Tool building tools" id="toolbuilders">
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68 <tool file="toolfactory/rgToolFactory.xml"/>
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69 </section>
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70
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71 If not already there (I just added it to datatypes_conf.xml.sample), please add:
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72 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
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73 to your local data_types_conf.xml.
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74 )
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75
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76 Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
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77 Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
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78 The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
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79
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80 * Restricted execution *
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81 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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82 **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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83 arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
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84 Galaxy data would probably be lack of appropriate technical skills.
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85
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86 *What it does* This is a tool factory for simple scripts in python, R and perl currently.
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87 Functional tests are automatically generated. How cool is that.
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88
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89 LIMITED to simple scripts that read one input from the history.
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90 Optionally can write one new history dataset,
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91 and optionally collect any number of outputs into links on an autogenerated HTML
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92 index page for the user to navigate - useful if the script writes images and output files - pdf outputs
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93 are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to
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94 be avaailable.
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95
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96 Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since
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97 a generated script gets you a serious leg up to a more complex one.
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98
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99 *What you do* You paste and run your script
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100 you fix the syntax errors and eventually it runs
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101 You can use the redo button and edit the script before
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102 trying to rerun it as you debug - it works pretty well.
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103
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104 Once the script works on some test data, you can
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105 generate a toolshed compatible gzip file
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106 containing your script ready to run as an ordinary Galaxy tool in a
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107 repository on your local toolshed. That means safe and largely automated installation in any
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108 production Galaxy configured to use your toolshed.
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109
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110 *Generated tool Security* Once you install a generated tool, it's just
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111 another tool - assuming the script is safe. They just run normally and their user cannot do anything unusually insecure
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112 but please, practice safe toolshed.
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113 Read the fucking code before you install any tool.
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114 Especially this one - it is really scary.
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115
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116 If you opt for an HTML output, you get all the script outputs arranged
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117 as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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118 Ugly but really inexpensive.
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119
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120 Patches and suggestions welcome as bitbucket issues please?
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121
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122 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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123
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124 all rights reserved
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125 Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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126
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127 Material for our more enthusiastic and voracious readers continues below - we salute you.
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128
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129 **Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
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130 - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
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131
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132 **Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
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133 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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134 tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
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135
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136 1. Install the tool factory on a personal private instance
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137
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138 2. Upload a small test data set
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139
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140 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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141 there is absolutely no reason to do this anywhere other than on a personal private instance.
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142
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143 4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
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144
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145 5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
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146
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147 6. Upload the new tool to the toolshed
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148
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149 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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150
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151 **Simple examples on the tool form**
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152
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153 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
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154 does something (transpose in this case) and writes the results to a new tabular file::
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155
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156 # transpose a tabular input file and write as a tabular output file
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157 ourargs = commandArgs(TRUE)
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158 inf = ourargs[1]
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159 outf = ourargs[2]
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160 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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161 outp = t(inp)
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162 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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163
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164 Calculate a multiple test adjusted p value from a column of p values - for this script to be useful,
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165 it needs the right column for the input to be specified in the code for the
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166 given input file type(s) specified when the tool is generated ::
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167
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168 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
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169 column = 1 # adjust if necessary for some other kind of input
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170 fdrmeth = 'BH'
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171 ourargs = commandArgs(TRUE)
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172 inf = ourargs[1]
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173 outf = ourargs[2]
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174 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
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175 p = inp[,column]
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176 q = p.adjust(p,method=fdrmeth)
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177 newval = paste(fdrmeth,'p-value',sep='_')
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178 q = data.frame(q)
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179 names(q) = newval
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180 outp = cbind(inp,newval=q)
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181 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
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182
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183
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184
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185 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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186 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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187
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188 # note this script takes NO input or output because it generates random data
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189 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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190 bar = as.matrix(foo)
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191 pdf( "heattest.pdf" )
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192 heatmap(bar,main='Random Heatmap')
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193 dev.off()
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194
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195 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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196 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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197 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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198
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199 # reverse order of columns in a tabular file
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200 import sys
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201 inp = sys.argv[1]
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202 outp = sys.argv[2]
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203 i = open(inp,'r')
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204 o = open(outp,'w')
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205 for row in i:
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206 rs = row.rstrip().split('\t')
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207 rs.reverse()
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208 o.write('\t'.join(rs))
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209 o.write('\n')
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210 i.close()
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211 o.close()
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212
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213
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214 Galaxy as an IDE for developing API scripts
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215 If you need to develop Galaxy API scripts and you like to live dangerously, please read on.
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216
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217 Galaxy as an IDE?
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218 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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219
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220 Why bother - what's wrong with Eclipse
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221 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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222
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223 Workflow
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224 Fire up the Tool Factory in Galaxy.
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225
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226 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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227
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228 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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229
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230 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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231
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232 Eg tool factory api script
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233 import sys
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234 from blend.galaxy import GalaxyInstance
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235 ourGal = 'http://x.x.x.x:xxxx'
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236 ourKey = 'xxx'
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237 gi = GalaxyInstance(ourGal, key=ourKey)
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238 libs = gi.libraries.get_libraries()
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239 res = []
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240 # libs looks like
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241 # u'url': u'/galaxy/api/libraries/441d8112651dc2f3', u'id': u'441d8112651dc2f3', u'name':.... u'Demonstration sample RNA data',
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242 for lib in libs:
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243 res.append('%s:\n' % lib['name'])
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244 res.append(str(gi.libraries.show_library(lib['id'],contents=True)))
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245 outf=open(sys.argv[2],'w')
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246 outf.write('\n'.join(res))
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247 outf.close()
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248
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249 **Attribution**
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250 Creating re-usable tools from scripts: The Galaxy Tool Factory
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251 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
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252 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
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253
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254 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
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255
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256 **Licensing**
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257 Copyright Ross Lazarus 2010
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258 ross lazarus at g mail period com
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259
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260 All rights reserved.
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261
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262 Licensed under the LGPL
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263
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264 **Obligatory screenshot**
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265
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266 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
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267