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Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
author bgruening
date Tue, 25 Jun 2013 04:33:41 -0400
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1 ===============================
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2 Galaxy wrapper for RepeatMasker
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3 ===============================
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4
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5 This wrapper is copyright 2013 by Björn Grüning.
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6
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7 This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology.
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8 http://www.repeatmasker.org/
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11 Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.
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12 1996-2010 <http://www.repeatmasker.org>.
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15 Additional Information:
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16 Using RepeatMasker to identify repetitive elements in genomic sequences.
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17 http://www.ncbi.nlm.nih.gov/pubmed/19274634
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19 ============
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20 Installation
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21 ============
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22
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23 To install RepeatMasker, please use the following instructions:
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25 http://www.repeatmasker.org/RMDownload.html
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27 To install the wrapper copy the file RepeatMasker.xml in the galaxy tools
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28 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
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29 Add a line like the following:
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31 Add the tool definition to your tool_conf.xml file under Galaxy root.
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32 <tool file="RepeatMasker/RepeatMasker.xml" />
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33
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34 =======
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35 History
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36 =======
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37
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38 - v1.1: Initial public release
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39 - v0.1.1: patch from Simon Guest, to create empty files if no repeat is found
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40 - v0.1.2: remove trailing semicolon, redirect all output to stdout
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42 ===============================
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43 Wrapper Licence (MIT/BSD style)
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44 ===============================
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45
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46 Permission to use, copy, modify, and distribute this software and its
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47 documentation with or without modifications and for any purpose and
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48 without fee is hereby granted, provided that any copyright notices
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49 appear in all copies and that both those copyright notices and this
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50 permission notice appear in supporting documentation, and that the
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51 names of the contributors or copyright holders not be used in
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52 advertising or publicity pertaining to distribution of the software
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53 without specific prior permission.
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54
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55 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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56 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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57 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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58 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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59 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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60 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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61 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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62 OR PERFORMANCE OF THIS SOFTWARE.
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