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comparison weblogo3-91fa0a8ce39d/rgweblogo/README @ 1:a76ecde597e1 draft

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author fubar
date Wed, 04 Dec 2013 19:58:06 -0500
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1 This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
2 Last updated by Ross to install iuc ghostscript and numpy dependencies.
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4 Weblogo generates sequence logos from fasta files such as the alignments generated by clustalw
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6 Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data
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8 **Automated Installation**
9 As a Galaxy admin, use the admin menu and select the search ToolShed option. This tool should be on the main toolshed - if not try the test toolshed.
10 Select it and choose "preview and install" - the process of downloading and installing weblogo3.3 and this wrapper should take a few minutes at most.
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12 ** Manual Installation**
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14 Don't.
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16 If you insist,
17 Make sure weblogo3 is installed in your system python and is available on the path for all your nodes
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19 Move the test data files to your galaxy root test-data
20 Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there.
21 Run
22 sh run_functional_tests.sh -id weblogo3
23 to make sure the tests work
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25 then restart Galaxy and you should be good to go.
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27
28 **Attribution**
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30 Source for the weblogo3 python executable is at http://weblogo.berkeley.edu
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32 Galaxy tool wrapper written by Ross Lazarus for the Rgenetics project
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34 Copyright Ross Lazarus at gmail com 2011
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36 All rights reserved.
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38 Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html