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1 VarScan2 mpileup2snp wrapper for Galaxy
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2 =======================================
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3
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4 http://sourceforge.net/projects/varscan/
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5
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6 This wrapper is optimized for direct access to BAM files such that the
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7 big mpileup files are not saved.
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8
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9 Development
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10 -----------
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11
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12 * Repository-Maintainer: Youri Hoogstrate
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13
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14 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
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15
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16 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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17 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
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18 Research IT (TraIT) project:
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19
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20 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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21
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22 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
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23
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24 http://toolshed.dtls.nl/
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25
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26 License
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27 -------
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28
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29 **VarScan2**:
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30
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31 Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0): http://sourceforge.net/directory/os:linux/license:nposl3/freshness:recently-updated/ http://opensource.org/licenses/NPOSL-3.0
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32
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33 **samtools**:
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34
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35 MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
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36
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37 The MIT/Expat License
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38
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39 Copyright (C) 2008-2014 Genome Research Ltd.
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40
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41 Permission is hereby granted, free of charge, to any person obtaining a copy
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42 of this software and associated documentation files (the "Software"), to deal
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43 in the Software without restriction, including without limitation the rights
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44 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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45 copies of the Software, and to permit persons to whom the Software is
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46 furnished to do so, subject to the following conditions:
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47
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48 The above copyright notice and this permission notice shall be included in
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49 all copies or substantial portions of the Software.
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50
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51 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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52 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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53 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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54 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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55 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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56 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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57 DEALINGS IN THE SOFTWARE.
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58
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59 [The use of a range of years within a copyright notice in this distribution
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60 should be interpreted as being equivalent to a list of years including the
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61 first and last year specified and all consecutive years between them.
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62
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63 For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
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64 2011-2012" should be interpreted as being identical to a notice that reads
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65 "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
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66 that reads "Copyright (C) 2005-2012" should be interpreted as being identical
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67 to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
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68 2011, 2012".]
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69
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70 **samtools-parallel-mpileup**:
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71
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72 MIT License: https://raw.githubusercontent.com/mydatascience/parallel-mpileup/master/samtools-0.1.19/COPYING
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73
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74 MIT License:
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75
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76 Copyright (c) 2008-2009 Genome Research Ltd.
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77
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78 Permission is hereby granted, free of charge, to any person obtaining a copy
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79 of this software and associated documentation files (the "Software"), to deal
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80 in the Software without restriction, including without limitation the rights
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81 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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82 copies of the Software, and to permit persons to whom the Software is
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83 furnished to do so, subject to the following conditions:
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85 The above copyright notice and this permission notice shall be included in
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86 all copies or substantial portions of the Software.
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87
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88 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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89 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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90 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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91 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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92 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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93 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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94 THE SOFTWARE.
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95
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96 **This wrapper**:
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97
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98 Copyright (C) 2013-2014 Youri Hoogstrate
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99
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100 This program is free software: you can redistribute it and/or modify
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101 it under the terms of the GNU General Public License as published by
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102 the Free Software Foundation, either version 3 of the License, or
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103 (at your option) any later version.
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104
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105 This program is distributed in the hope that it will be useful,
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106 but WITHOUT ANY WARRANTY; without even the implied warranty of
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107 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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108 GNU General Public License for more details.
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109
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110 You should have received a copy of the GNU General Public License
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111 along with this program. If not, see <http://www.gnu.org/licenses/>.
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