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author fubar
date Thu, 11 Jul 2013 00:08:05 -0400
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1 Updated july 11 2013 for automated toolshed installation
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3 ** This is a wrapper for ClustalW **
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5 This tool allows you to align multiple sequences in Galaxy, using ClustalW2_ with mostly default options which should work reasonably well for many alignments.
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6 DNA or protein sequences can be aligned. The input file must be a fasta file in your current history.
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8 The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history and a text log will be output to your history
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9 showing the output Clustalw would normally write to standard output.
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11 If Clustal format is chosen, you have the option of adding basepair counts to the output
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13 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output
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15 **Installation**
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17 As of July 2013, automated installation from the tool shed should have worked.
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19 Otherwise, the old skool way was:
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21 Make sure clustalw2 is available on the path for all your nodes
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23 Move the test data files to your galaxy root test-data
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24 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.
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25 Run
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26 sh run_functional_tests.sh -id clustalw
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27 to make sure the tests work
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29 then restart Galaxy and you should be good to go.
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31 **Attribution**
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33 Clustal attribution and associated documentation are available at http://www.clustal.org
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35 An implementation of a Galaxy Clustal wrapper was written by Hans-Rudolf Hotz in an email on the developer list -
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36 http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
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38 This version by Ross Lazarus for the rgenetics project, builds on Hans-Rudolf's code, adding some additional controls and a log file. It also
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39 deals with stderr so Cluastalw2 writing there doesn't cause the job to error out. That's encoded in the tail of the command line.
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41 **License**
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43 Assuming Hans-Rudolf is ok with a new license for this derived work, this version of his wrapper is LGPL like other rgenetics artefacts
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45 Written by Ross Lazarus for the Rgenetics project
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47 Copyright Ross Lazarus at gmail com 2011
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49 All rights reserved.
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51 Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html
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