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author fubar
date Sun, 01 Mar 2015 05:57:52 -0500
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1 # WARNING before you start 1 # WARNING before you start
2 # Install this tool on a private Galaxy ONLY 2 # Install this tool on a private Galaxy ONLY
3 # Please NEVER on a public or production instance 3 # Please NEVER on a public or production instance
4 # updated august 2014 by John Chilton adding citation support
5 #
4 # updated august 8 2014 to fix bugs reported by Marius van den Beek 6 # updated august 8 2014 to fix bugs reported by Marius van den Beek
5 Please cite: 7 # please cite the resource at http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
6 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref 8 # if you use this tool in your published work.
7 if you use this tool in your published work.
8 9
9 *Short Story* 10 *Short Story*
10 11
11 This is an unusual Galaxy tool that exposes unrestricted and therefore extremely dangerous 12 This is an unusual Galaxy tool capable of generating new Galaxy tools.
12 scripting to designated administrative users of a Galaxy server, allowing them to run scripts 13 It works by exposing *unrestricted* and therefore extremely dangerous
13 in R, python, sh and perl over a single input data set, writing a single new data set as output. 14 scripting to all designated administrators of the host Galaxy server, allowing them to run scripts
14 15 in R, python, sh and perl over multiple selected input data sets, writing a single new data set as output.
15 In addition, this tool optionally generates very simple new Galaxy tools, that effectively 16
16 freeze the supplied script into a new, ordinary Galaxy tool that runs it over a single input file, 17 *Automated outputs in named sections*
17 working just like any other Galaxy tool for your users. 18
19 If your script writes to the current directory path, arbitrary mix of (eg) pdfs, tabular analysis results and run logs,
20 the tool factory can optionally auto-generate a linked Html page with separate sections showing a thumbnail grid
21 for all pdfs and the log text, grouping all artifacts sharing a file name and log name prefix::
22
23 eg: if "foo.log" is emitted then *all* other outputs matching foo_* will all be grouped together - eg
24 foo_baz.pdf
25 foo_bar.pdf and
26 foo_zot.xls
27 would all be displayed and linked in the same section with foo.log's contents - to form the "Foo" section of the Html page.
28 Sections appear in alphabetic order and there are no limits on the number of files or sections.
29
30 *Automated generation of new Galaxy tool shed tools for installation into any Galaxy*
31
32 Once a script is working correctly, this tool optionally generates a new Galaxy tool, effectively
33 freezing the supplied script into a new, ordinary Galaxy tool that runs it over one or more input files
34 selected by the user. Generated tools are installed via a tool shed by an administrator and work exactly like all other Galaxy tools for your users.
18 35
19 If you use the Html output option, please ensure that sanitize_all_html is set to False and 36 If you use the Html output option, please ensure that sanitize_all_html is set to False and
20 uncommented in universe_wsgi.ini - it should show: 37 uncommented in universe_wsgi.ini - it should show::
21 38
22 # By default, all tool output served as 'text/html' will be sanitized 39 # By default, all tool output served as 'text/html' will be sanitized
23 sanitize_all_html = False 40 sanitize_all_html = False
41
42 This opens potential security risks and may not be acceptable for public sites where the lack of stylesheets
43 may make Html pages damage onlookers' eyeballs but should still be correct.
44
24 45
25 *More Detail* 46 *More Detail*
26 47
27 To use the ToolFactory, you should have prepared a script to paste into a text box, 48 To use the ToolFactory, you should have prepared a script to paste into a text box,
28 and a small test input example ready to select from your history to test your new script. 49 and a small test input example ready to select from your history to test your new script.
75 Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters. 96 Of course, R, python, perl etc are needed on your path if you want to test scripts using those interpreters.
76 Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code. 97 Adding new ones to this tool code should be easy enough. Please make suggestions as bitbucket issues and code.
77 The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick . 98 The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick .
78 99
79 * Restricted execution * 100 * Restricted execution *
80 The new tool factory tool will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini 101 The tool factory tool itself will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini
81 **Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any 102 **Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any
82 arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your 103 arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your
83 Galaxy data would probably be lack of appropriate technical skills. 104 Galaxy data would probably be lack of appropriate technical skills.
84 105
85 *What it does* This is a tool factory for simple scripts in python, R and perl currently. 106 *What it does* This is a tool factory for simple scripts in python, R and perl currently.