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comparison toolfactory/test-data/input1_sample @ 62:881bd8c81ac9 draft

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1 *WARNING before you start*
2
3 Install this tool on a private Galaxy ONLY
4 Please NEVER on a public or production instance
5
6 Updated august 2014 by John Chilton adding citation support
7
8 Updated august 8 2014 to fix bugs reported by Marius van den Beek
9
10 Please cite the resource at
11 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
12 if you use this tool in your published work.
13
14 **Short Story**
15
16 This is an unusual Galaxy tool capable of generating new Galaxy tools.
17 It works by exposing *unrestricted* and therefore extremely dangerous scripting
18 to all designated administrators of the host Galaxy server, allowing them to
19 run scripts in R, python, sh and perl over multiple selected input data sets,
20 writing a single new data set as output.
21
22 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
23
24 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
25
26
27 **Automated generation of new Galaxy tools for installation into any Galaxy**
28
29 A test is generated using small sample test data inputs and parameter settings you supply.
30 Once the test case outputs have been produced, they can be used to build a
31 new Galaxy tool. The supplied script or executable is baked as a requirement
32 into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
33 Generated tools are installed via a tool shed by an administrator
34 and work exactly like all other Galaxy tools for your users.
35
36 **More Detail**
37
38 To use the ToolFactory, you should have prepared a script to paste into a
39 text box, or have a package in mind and a small test input example ready to select from your history
40 to test your new script.
41
42 ```planemo test rgToolFactory2.xml --galaxy_root ~/galaxy --test_data ~/galaxy/tools/tool_makers/toolfactory/test-data``` works for me
43
44 There is an example in each scripting language on the Tool Factory form. You
45 can just cut and paste these to try it out - remember to select the right
46 interpreter please. You'll also need to create a small test data set using
47 the Galaxy history add new data tool.
48
49 If the script fails somehow, use the "redo" button on the tool output in
50 your history to recreate the form complete with broken script. Fix the bug
51 and execute again. Rinse, wash, repeat.
52
53 Once the script runs sucessfully, a new Galaxy tool that runs your script
54 can be generated. Select the "generate" option and supply some help text and
55 names. The new tool will be generated in the form of a new Galaxy datatype
56 *toolshed.gz* - as the name suggests, it's an archive ready to upload to a
57 Galaxy ToolShed as a new tool repository.
58
59 Once it's in a ToolShed, it can be installed into any local Galaxy server
60 from the server administrative interface.
61
62 Once the new tool is installed, local users can run it - each time, the script
63 that was supplied when it was built will be executed with the input chosen
64 from the user's history. In other words, the tools you generate with the
65 ToolFactory run just like any other Galaxy tool,but run your script every time.
66
67 Tool factory tools are perfect for workflow components. One input, one output,
68 no variables.
69
70 *To fully and safely exploit the awesome power* of this tool,
71 Galaxy and the ToolShed, you should be a developer installing this
72 tool on a private/personal/scratch local instance where you are an
73 admin_user. Then, if you break it, you get to keep all the pieces see
74 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
75
76 **Installation**
77 This is a Galaxy tool. You can install it most conveniently using the
78 administrative "Search and browse tool sheds" link. Find the Galaxy Main
79 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
80 repository. Open it and review the code and select the option to install it.
81
82 If you can't get the tool that way, the xml and py files here need to be
83 copied into a new tools
84 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
85 pointing to the xml
86 file - something like::
87
88 <section name="Tool building tools" id="toolbuilders">
89 <tool file="toolfactory/rgToolFactory.xml"/>
90 </section>
91
92 If not already there,
93 please add:
94 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
95 mimetype="multipart/x-gzip" subclass="True" />
96 to your local data_types_conf.xml.
97
98
99 **Restricted execution**
100
101 The tool factory tool itself will then be usable ONLY by admin users -
102 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
103 admin_users can run this tool** Think about it for a moment. If allowed to
104 run any arbitrary script on your Galaxy server, the only thing that would
105 impede a miscreant bent on destroying all your Galaxy data would probably
106 be lack of appropriate technical skills.
107
108 **What it does**
109
110 This is a tool factory for simple scripts in python, R and
111 perl currently. Functional tests are automatically generated. How cool is that.
112
113 LIMITED to simple scripts that read one input from the history. Optionally can
114 write one new history dataset, and optionally collect any number of outputs
115 into links on an autogenerated HTML index page for the user to navigate -
116 useful if the script writes images and output files - pdf outputs are shown
117 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
118 imagemagik need to be available.
119
120 Generated tools can be edited and enhanced like any Galaxy tool, so start
121 small and build up since a generated script gets you a serious leg up to a
122 more complex one.
123
124 **What you do**
125
126 You paste and run your script, you fix the syntax errors and
127 eventually it runs. You can use the redo button and edit the script before
128 trying to rerun it as you debug - it works pretty well.
129
130 Once the script works on some test data, you can generate a toolshed compatible
131 gzip file containing your script ready to run as an ordinary Galaxy tool in
132 a repository on your local toolshed. That means safe and largely automated
133 installation in any production Galaxy configured to use your toolshed.
134
135 **Generated tool Security**
136
137 Once you install a generated tool, it's just
138 another tool - assuming the script is safe. They just run normally and their
139 user cannot do anything unusually insecure but please, practice safe toolshed.
140 Read the code before you install any tool. Especially this one - it is really scary.
141
142 **Send Code**
143
144 Patches and suggestions welcome as bitbucket issues please?
145
146 **Attribution**
147
148 Creating re-usable tools from scripts: The Galaxy Tool Factory
149 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
150 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
151
152 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
153
154 **Licensing**
155
156 Copyright Ross Lazarus 2010
157 ross lazarus at g mail period com
158
159 All rights reserved.
160
161 Licensed under the LGPL
162
163 **Obligatory screenshot**
164
165 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
166