Mercurial > repos > fubar > toolfactory
comparison README.txt @ 45:7b34711416d2 draft
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author | fubar |
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date | Sun, 01 Mar 2015 05:57:52 -0500 |
parents | 8d28e32c71ff |
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44:417cba94d862 | 45:7b34711416d2 |
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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. |