Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

comparison rgToolFactory.xml @ 25:8cc3f3c0e539 default tip

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Now uses admin_users to check that the user is authorized to run this tool Docs adjusted.
author Ross Lazarus <ross.lazarus@gmail.com>
date Wed, 06 Jun 2012 14:16:25 +1000
parents 8289ebc513ab
children
comparison
equal deleted inserted replaced
24:8289ebc513ab 25:8cc3f3c0e539
1 <tool id="rgTF" name="Tool Factory" version="0.05"> 1 <tool id="rgTF" name="Tool Factory" version="0.05">
2 <description>Makes scripts into tools</description> 2 <description>Makes scripts into tools</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 #if ( $__user_email__ not in ['yourID@email','ross.lazarus@gmail.com'] ): 4 #if ( $__user_email__ not in $__admin_users__ ):
5 rgToolFactory.py --bad_user $__user_email__ 5 rgToolFactory.py --bad_user $__user_email__
6 #else: 6 #else:
7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 7 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
8 --tool_name "$tool_name" 8 --tool_name "$tool_name"
9 #if $make_TAB.value=="yes": 9 #if $make_TAB.value=="yes":
109 ${makeMode.help_text} 109 ${makeMode.help_text}
110 #end if 110 #end if
111 </configfile> 111 </configfile>
112 </configfiles> 112 </configfiles>
113 <help> 113 <help>
114
115 .. class:: warningmark
116
117 **Local Admins ONLY** Only users whose IDs found in the local admin_user configuration setting in universe_wsgi.ini can run this tool.
118
114 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy. 119 **What it does** This tool enables a user to paste and submit an arbitrary R/python/perl script to Galaxy.
115 120
116 **Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history. 121 **Input options** This version is limited to simple transformation or reporting requiring only a single input file selected from the history.
117 122
118 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs, 123 **Output options** Optional script outputs include one single new history tabular file, or for scripts that create multiple outputs,
119 a new HTML report linking all the files and images created by the script can be automatically generated. 124 a new HTML report linking all the files and images created by the script can be automatically generated.
120 125
121 **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file 126 **Tool Generation option** Once the script is working with test data, this tool will optionally generate a new Galaxy tool in a gzip file
122 ready to upload to your local toolshed for sharing and installation. 127 ready to upload to your local toolshed for sharing and installation.
123 128
124 **Permission to to use this tool** must be explicitly granted by an administrator adding approved Galaxy user IDs to the local tool XML list of permitted users. *It will not run otherwise*
125
126 .. class:: warningmark 129 .. class:: warningmark
127 130
128 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts and should only be installed on private/personnal Galaxy instances. 131 **Note to system administrators** This tool offers *NO* built in protection against malicious scripts. It should only be installed on private/personnal Galaxy instances.
129 Under no circumstances should you allow any user to use this tool unless you really, really trust them with the power to do what they want as the Galaxy user. 132 Admin_users will have the power to do anything they want as the Galaxy user if you install this tool.
130 133
131 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation. 134 The tools generated by this tool will run just as securely as any other normal installed Galaxy tool but like any other new tools, should always be checked carefully before installation.
135 We recommend that you follow the good code hygiene practices associated with safe toolshed.
132 136
133 .. class:: warningmark 137 .. class:: warningmark
134 138
135 **Use on public servers** is STRONGLY discouraged for obvious reasons 139 **Use on public servers** is STRONGLY discouraged for obvious reasons
136 140