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comparison toolfactory/README.md @ 43:e7e9732ebed6 draft

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1 Note as at August 8 2020
2
3
4 *WARNING before you start*
5
6 Install this tool on a private Galaxy ONLY
7 Please NEVER on a public or production instance
8
9 Please cite the resource at
10 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
11 if you use this tool in your published work.
12
13 **Short Story**
14
15 This is an unusual Galaxy tool capable of generating new Galaxy tools.
16 It works by exposing *unrestricted* and therefore extremely dangerous scripting
17 to all designated administrators of the host Galaxy server, allowing them to
18 run scripts in R, python, sh and perl over multiple selected input data sets,
19 writing a single new data set as output.
20
21 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
22
23 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
24
25 **Automated generation of new Galaxy tools for installation into any Galaxy**
26
27 A test is generated using small sample test data inputs and parameter settings you supply.
28 Once the test case outputs have been produced, they can be used to build a
29 new Galaxy tool. The supplied script or executable is baked as a requirement
30 into a new, ordinary Galaxy tool, fully workflow compatible out of the box.
31 Generated tools are installed via a tool shed by an administrator
32 and work exactly like all other Galaxy tools for your users.
33
34 **More Detail**
35
36 To use the ToolFactory, you should have prepared a script to paste into a
37 text box, or have a package in mind and a small test input example ready to select from your history
38 to test your new script.
39
40 ```planemo test --no_cleanup --no_dependency_resolution --skip_venv --galaxy_root ~/galaxy ~/rossgit/toolfactory``` works for me
41
42 There is an example in each scripting language on the Tool Factory form. You
43 can just cut and paste these to try it out - remember to select the right
44 interpreter please. You'll also need to create a small test data set using
45 the Galaxy history add new data tool.
46
47 If the script fails somehow, use the "redo" button on the tool output in
48 your history to recreate the form complete with broken script. Fix the bug
49 and execute again. Rinse, wash, repeat.
50
51 Once the script runs sucessfully, a new Galaxy tool that runs your script
52 can be generated. Select the "generate" option and supply some help text and
53 names. The new tool will be generated in the form of a new Galaxy datatype
54 *tgz* - as the name suggests, it's an archive ready to upload to a
55 Galaxy ToolShed as a new tool repository.
56
57
58 Once it's in a ToolShed, it can be installed into any local Galaxy server
59 from the server administrative interface.
60
61 Once the new tool is installed, local users can run it - each time, the script
62 that was supplied when it was built will be executed with the input chosen
63 from the user's history. In other words, the tools you generate with the
64 ToolFactory run just like any other Galaxy tool,but run your script every time.
65
66 Tool factory tools are perfect for workflow components. One input, one output,
67 no variables.
68
69 *To fully and safely exploit the awesome power* of this tool,
70 Galaxy and the ToolShed, you should be a developer installing this
71 tool on a private/personal/scratch local instance where you are an
72 admin_user. Then, if you break it, you get to keep all the pieces see
73 https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
74
75 **Installation**
76 This is a Galaxy tool. You can install it most conveniently using the
77 administrative "Search and browse tool sheds" link. Find the Galaxy Main
78 toolshed at https://toolshed.g2.bx.psu.edu/ and search for the toolfactory
79 repository. Open it and review the code and select the option to install it.
80
81 If you can't get the tool that way, the xml and py files here need to be
82 copied into a new tools
83 subdirectory such as tools/toolfactory Your tool_conf.xml needs a new entry
84 pointing to the xml
85 file - something like::
86
87 <section name="Tool building tools" id="toolbuilders">
88 <tool file="toolfactory/rgToolFactory.xml"/>
89 </section>
90
91 If not already there,
92 please add:
93 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary"
94 mimetype="multipart/x-gzip" subclass="True" />
95 to your local data_types_conf.xml.
96
97
98 **Restricted execution**
99
100 The tool factory tool itself will then be usable ONLY by admin users -
101 people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY
102 admin_users can run this tool** Think about it for a moment. If allowed to
103 run any arbitrary script on your Galaxy server, the only thing that would
104 impede a miscreant bent on destroying all your Galaxy data would probably
105 be lack of appropriate technical skills.
106
107 **What it does**
108
109 This is a tool factory for simple scripts in python, R and
110 perl currently. Functional tests are automatically generated.
111
112 LIMITED to simple scripts that read one input from the history. Optionally can
113 write one new history dataset, and optionally collect any number of outputs
114 into links on an autogenerated HTML index page for the user to navigate -
115 useful if the script writes images and output files - pdf outputs are shown
116 as thumbnails and R's bloated pdf's are shrunk with ghostscript so that and
117 imagemagik need to be available.
118
119 Generated tools can be edited and enhanced like any Galaxy tool, so start
120 small and build up since a generated script gets you a serious leg up to a
121 more complex one.
122
123 **What you do**
124
125 You paste and run your script, you fix the syntax errors and
126 eventually it runs. You can use the redo button and edit the script before
127 trying to rerun it as you debug - it works pretty well.
128
129 Once the script works on some test data, you can generate a toolshed compatible
130 gzip file containing your script ready to run as an ordinary Galaxy tool in
131 a repository on your local toolshed. That means safe and largely automated
132 installation in any production Galaxy configured to use your toolshed.
133
134 **Generated tool Security**
135
136 Once you install a generated tool, it's just
137 another tool - assuming the script is safe. They just run normally and their
138 user cannot do anything unusually insecure but please, practice safe toolshed.
139 Read the code before you install any tool. Especially this one - it is really scary.
140
141 **Send Code**
142
143 Patches and suggestions welcome as bitbucket issues please?
144
145 **Attribution**
146
147 Creating re-usable tools from scripts: The Galaxy Tool Factory
148 Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team
149 Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573
150
151 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
152
153 **Licensing**
154
155 Copyright Ross Lazarus 2010
156 ross lazarus at g mail period com
157
158 All rights reserved.
159
160 Licensed under the LGPL
161
162 **Obligatory screenshot**
163
164 http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png
165