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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
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24:8289ebc513ab 25:8cc3f3c0e539
9 You don't have enough developer resources for wrapping dozens of even relatively simple tools; 9 You don't have enough developer resources for wrapping dozens of even relatively simple tools;
10 Your institution would be better off if those nasty, feral scripts were all tucked safely in 10 Your institution would be better off if those nasty, feral scripts were all tucked safely in
11 a local toolshed. 11 a local toolshed.
12 12
13 *The good news* If it can be trivially scripted, it can be running safely in your 13 *The good news* If it can be trivially scripted, it can be running safely in your
14 local Galaxy via your own local toolshed. 14 local Galaxy via your own local toolshed in a few minutes.
15
15 That's what this tool does. You paste a simple script and the tool returns 16 That's what this tool does. You paste a simple script and the tool returns
16 a new, real Galaxy tool, ready to be installed from the local toolshed to local servers. 17 a new, real Galaxy tool, ready to be installed from the local toolshed to local servers.
17 Scripts can be wrapped and online literally within minutes. 18 Scripts can be wrapped and online literally within minutes.
18 19
19 *To fully and safely exploit the awesome power* of Galaxy with this tool installed 20 *To fully and safely exploit the awesome power* of this tool, Galaxy and the ToolShed,
20 you should be a developer installing this tool on a 21 you should be a developer installing this tool on a private/personal/scratch local instance where you are an admin_user.
21 personal/scratch local instance - ie a private site 22 Then, if you break it, you get to keep all the pieces
22 because then, if you break it, you get to keep all the pieces
23 see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home 23 see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
24 24
25 *To make the tool work* Ghostscript and imagemagick MUST be installed, and if not already there, please add: 25 *To make the tool work* R, python, perl etc are needed on your path if you want to run scripts using those interpreters.
26 The HTML file code to shrink R's gross pdfs requires Ghostscript and imagemagick must be installed for generating the thumbnails.
27 If not already there (I just added it to datatypes_conf.xml.sample), please add:
26 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /> 28 <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
27 to your local data_types_conf.xml and PUT some real IDs in the list in the XML before you restart Galaxy to load this new tool please 29 to your local data_types_conf.xml.
28 otherwise, the tool won't run for anybody. 30
31 **Note that ONLY admin_users can run this tool**
29 32
30 *What it does* This is a tool factory for simple scripts in python, R or whatever ails ye. 33 *What it does* This is a tool factory for simple scripts in python, R or whatever ails ye.
31 LIMITED to simple scripts that read one input from the history. 34 LIMITED to simple scripts that read one input from the history.
32 Optionally can write one new history dataset, 35 Optionally can write one new history dataset,
33 and optionally collect any number of outputs into links on an autogenerated HTML page. 36 and optionally collect any number of outputs into links on an autogenerated HTML page.