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annotate fubar-galaxytoolfactory-2e68c2a22b43/README.txt @ 2:b55b59435fb1 draft

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Now with bash working I think. Special case but working..
author fubar
date Mon, 13 Aug 2012 06:27:26 -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
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5 *Short Story*
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6 This is an unusual Galaxy tool that generates very simple new Galaxy tools that run the user
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7 a supplied script (R, python, perl, bash...) over a single input file.
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8 Whenever you run this tool, the ToolFactory, you should have prepared a script to paste into a text box,
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9 and a small test input example ready to select from your history to test your new script
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10
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11 If the script runs sucessfully, a new Galaxy tool that runs your script can be generated.
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12 The new tool is in the form of a special new Galaxy datatype - toolshed.gz - as the name suggests,
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13 it's an archive ready to upload to a Galaxy ToolShed as a new tool repository.
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14
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15 Once it's in a ToolShed, it can be installed into any local Galaxy server from
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16 the server administrative interface.
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17
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18 Once your new tool is installed, local users can run it - each time, the script that was supplied
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19 when it was built will be executed with the input chosen from the user's history. In other words,
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20 the tools you generate with the ToolFactory run just like any other Galaxy tool,
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21 but run your script every time.
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22
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23 *Reasons to read further*
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24
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25 If you use Galaxy to support your research;
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26
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27 You and fellow users are sometimes forced to take data out of Galaxy, process it with ugly
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28 little perl/awk/sed/R... scripts and put it back;
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29
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30 You do this when you can't do some transformation in Galaxy (the 90/10 rule);
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31
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32 You don't have enough developer resources for wrapping dozens of even relatively simple tools;
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33
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34 Your research and your institution would be far better off if those feral scripts were all tucked safely in
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35 your local toolshed and Galaxy histories.
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36
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37 *The good news* If it can be trivially scripted, it can be running safely in your
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38 local Galaxy via your own local toolshed in a few minutes - with functional tests.
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40
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41 *Value proposition* The ToolFactory allows Galaxy to efficiently take over most of your lab's dark script matter,
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42 making it reproducible in Galaxy and shareable through the ToolShed.
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43
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44 That's what this tool does. You paste a simple script and the tool returns
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45 a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
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46 Scripts can be wrapped and online literally within minutes.
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47
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48 *To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
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49 you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user.
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50 Then, if you break it, you get to keep all the pieces
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51 see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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52
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53 ** Installation **
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54 This is a Galaxy tool. You can install it most conveniently using the administrative "Search and browse tool sheds" link.
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55 Find the Galaxy Test toolshed (not main) and search for the toolfactory repository.
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56 Open it and review the code and select the option to install it.
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57
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58 If you can't get the tool that way, the xml and py files here need to be copied into a new tools subdirectory such as tools/toolfactory
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59 Your tool_conf.xml needs a new entry pointing to the xml file - something like::
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60
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61 <section name="Tool building tools" id="toolbuilders">
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62 <tool file="toolfactory/rgToolFactory.xml"/>
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63 </section>
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64
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65 If not already there (I just added it to datatypes_conf.xml.sample), please add:
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66 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
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67 to your local data_types_conf.xml.
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68
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69 Ensure that html sanitization is set to False and uncommented in universe_wsgi.ini
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70
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71 You'll have to restart the server for the new tool to be available.
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72
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73 Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
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74 Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
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75 The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
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76
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77 * Restricted execution *
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78 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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79 **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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80 arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
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81 Galaxy data would probably be lack of appropriate technical skills.
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82
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83 *What it does* This is a tool factory for simple scripts in python, R and perl currently.
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84 Functional tests are automatically generated. How cool is that.
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85
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86 LIMITED to simple scripts that read one input from the history.
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87 Optionally can write one new history dataset,
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88 and optionally collect any number of outputs into links on an autogenerated HTML
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89 index page for the user to navigate - useful if the script writes images and output files - pdf outputs
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90 are shown as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and imagemagik need to
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91 be avaailable.
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92
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93 Generated tools can be edited and enhanced like any Galaxy tool, so start small and build up since
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94 a generated script gets you a serious leg up to a more complex one.
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95
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96 *What you do* You paste and run your script
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97 you fix the syntax errors and eventually it runs
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98 You can use the redo button and edit the script before
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99 trying to rerun it as you debug - it works pretty well.
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100
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101 Once the script works on some test data, you can
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102 generate a toolshed compatible gzip file
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103 containing your script ready to run as an ordinary Galaxy tool in a
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104 repository on your local toolshed. That means safe and largely automated installation in any
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105 production Galaxy configured to use your toolshed.
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106
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107 *Generated tool Security* Once you install a generated tool, it's just
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108 another tool - assuming the script is safe. They just run normally and their user cannot do anything unusually insecure
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109 but please, practice safe toolshed.
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110 Read the fucking code before you install any tool.
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111 Especially this one - it is really scary.
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112
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113 If you opt for an HTML output, you get all the script outputs arranged
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114 as a single Html history item - all output files are linked, thumbnails for all the pdfs.
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115 Ugly but really inexpensive.
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116
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117 Patches and suggestions welcome as bitbucket issues please?
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118
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119 long route to June 2012 product
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120 derived from an integrated script model
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121 called rgBaseScriptWrapper.py
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122 Note to the unwary:
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123 This tool allows arbitrary scripting on your Galaxy as the Galaxy user
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124 There is nothing stopping a malicious user doing whatever they choose
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125 Extremely dangerous!!
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126 Totally insecure. So, trusted users only
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127
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128
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129
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130
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131 copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
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132
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133 all rights reserved
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134 Licensed under the LGPL if you want to improve it, feel free https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
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135
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136 Material for our more enthusiastic and voracious readers continues below - we salute you.
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137
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138 **Motivation** Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
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139 - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
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140
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141 **Benefits** For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
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142 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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143 tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
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144
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145 1. Install the tool factory on a personal private instance
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146
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147 2. Upload a small test data set
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148
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149 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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150 there is absolutely no reason to do this anywhere other than on a personal private instance.
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151
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152 4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
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153
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154 5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
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155
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156 6. Upload the new tool to the toolshed
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157
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158 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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159
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160 **Simple examples on the tool form**
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161
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162 A simple Rscript "filter" showing how the command line parameters can be handled, takes an input file,
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163 does something (transpose in this case) and writes the results to a new tabular file::
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164
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165 # transpose a tabular input file and write as a tabular output file
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166 ourargs = commandArgs(TRUE)
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167 inf = ourargs[1]
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168 outf = ourargs[2]
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169 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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170 outp = t(inp)
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171 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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172
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173 Calculate a multiple test adjusted p value from a column of p values - for this script to be useful,
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174 it needs the right column for the input to be specified in the code for the
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175 given input file type(s) specified when the tool is generated ::
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176
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177 # use p.adjust - assumes a HEADER row and column 1 - please fix for any real use
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178 column = 1 # adjust if necessary for some other kind of input
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179 fdrmeth = 'BH'
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180 ourargs = commandArgs(TRUE)
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181 inf = ourargs[1]
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182 outf = ourargs[2]
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183 inp = read.table(inf,head=T,row.names=NULL,sep='\t')
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184 p = inp[,column]
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185 q = p.adjust(p,method=fdrmeth)
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186 newval = paste(fdrmeth,'p-value',sep='_')
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187 q = data.frame(q)
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188 names(q) = newval
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189 outp = cbind(inp,newval=q)
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190 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=T)
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191
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192
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193
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194 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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195 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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196
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197 # note this script takes NO input or output because it generates random data
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198 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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199 bar = as.matrix(foo)
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200 pdf( "heattest.pdf" )
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201 heatmap(bar,main='Random Heatmap')
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202 dev.off()
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203
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204 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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205 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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206 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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207
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208 # reverse order of columns in a tabular file
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209 import sys
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210 inp = sys.argv[1]
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211 outp = sys.argv[2]
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212 i = open(inp,'r')
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213 o = open(outp,'w')
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214 for row in i:
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215 rs = row.rstrip().split('\t')
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216 rs.reverse()
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217 o.write('\t'.join(rs))
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218 o.write('\n')
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219 i.close()
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220 o.close()
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221
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222
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223 **Attribution** Copyright Ross Lazarus (ross period lazarus at gmail period com) May 2012
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224
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225 All rights reserved.
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226
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227 Licensed under the LGPL
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228
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229
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230 **Obligatory screenshot**
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231
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232 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
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233