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README.txt rgToolFactory.py rgToolFactory.xml |
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diff -r 417cba94d862 -r 7b34711416d2 README.txt --- a/README.txt Tue Oct 07 20:23:23 2014 -0400 +++ b/README.txt Sun Mar 01 05:57:52 2015 -0500 |
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@@ -1,26 +1,47 @@ # WARNING before you start # Install this tool on a private Galaxy ONLY # Please NEVER on a public or production instance +# updated august 2014 by John Chilton adding citation support +# # updated august 8 2014 to fix bugs reported by Marius van den Beek -Please cite: -http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref -if you use this tool in your published work. +# please cite the resource at http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref +# if you use this tool in your published work. *Short Story* -This is an unusual Galaxy tool that exposes unrestricted and therefore extremely dangerous -scripting to designated administrative users of a Galaxy server, allowing them to run scripts -in R, python, sh and perl over a single input data set, writing a single new data set as output. +This is an unusual Galaxy tool capable of generating new Galaxy tools. +It works by exposing *unrestricted* and therefore extremely dangerous +scripting to all designated administrators of the host Galaxy server, allowing them to run scripts +in R, python, sh and perl over multiple selected input data sets, writing a single new data set as output. + +*Automated outputs in named sections* + +If your script writes to the current directory path, arbitrary mix of (eg) pdfs, tabular analysis results and run logs, +the tool factory can optionally auto-generate a linked Html page with separate sections showing a thumbnail grid +for all pdfs and the log text, grouping all artifacts sharing a file name and log name prefix:: -In addition, this tool optionally generates very simple new Galaxy tools, that effectively -freeze the supplied script into a new, ordinary Galaxy tool that runs it over a single input file, -working just like any other Galaxy tool for your users. + eg: if "foo.log" is emitted then *all* other outputs matching foo_* will all be grouped together - eg + foo_baz.pdf + foo_bar.pdf and + foo_zot.xls + would all be displayed and linked in the same section with foo.log's contents - to form the "Foo" section of the Html page. + Sections appear in alphabetic order and there are no limits on the number of files or sections. + +*Automated generation of new Galaxy tool shed tools for installation into any Galaxy* + +Once a script is working correctly, this tool optionally generates a new Galaxy tool, effectively +freezing the supplied script into a new, ordinary Galaxy tool that runs it over one or more input files +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. If you use the Html output option, please ensure that sanitize_all_html is set to False and -uncommented in universe_wsgi.ini - it should show: +uncommented in universe_wsgi.ini - it should show:: -# By default, all tool output served as 'text/html' will be sanitized -sanitize_all_html = False + # By default, all tool output served as 'text/html' will be sanitized + sanitize_all_html = False + +This opens potential security risks and may not be acceptable for public sites where the lack of stylesheets +may make Html pages damage onlookers' eyeballs but should still be correct. + *More Detail* @@ -77,7 +98,7 @@ The HTML file code automatically shrinks R's bloated pdfs, and depends on ghostscript. The thumbnails require imagemagick . * Restricted execution * -The new tool factory tool will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini +The tool factory tool itself will then be usable ONLY by admin users - people with IDs in admin_users in universe_wsgi.ini **Yes, that's right. ONLY admin_users can run this tool** Think about it for a moment. If allowed to run any arbitrary script on your Galaxy server, the only thing that would impede a miscreant bent on destroying all your Galaxy data would probably be lack of appropriate technical skills. |
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diff -r 417cba94d862 -r 7b34711416d2 rgToolFactory.py --- a/rgToolFactory.py Tue Oct 07 20:23:23 2014 -0400 +++ b/rgToolFactory.py Sun Mar 01 05:57:52 2015 -0500 |
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@@ -645,8 +645,8 @@ retval = self.runBash() else: if self.opts.output_dir: - ste = open(self.elog,'w') - sto = open(self.tlog,'w') + ste = open(self.elog,'a') + sto = open(self.tlog,'a') sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) sto.flush() p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) |
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diff -r 417cba94d862 -r 7b34711416d2 rgToolFactory.xml --- a/rgToolFactory.xml Tue Oct 07 20:23:23 2014 -0400 +++ b/rgToolFactory.xml Sun Mar 01 05:57:52 2015 -0500 |
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@@ -10,7 +10,7 @@ #else: rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" --tool_name "$tool_name" --user_email "$__user_email__" - #if $make_TAB=="yes": + #if $make_TAB.value=="yes": --output_tab "$tab_file" --output_format "$output_format" #end if @@ -24,7 +24,7 @@ --include_dependencies "yes" #end if - #if $make_HTML=="yes": + #if $make_HTML.value=="yes": --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" #else: --output_dir "." |