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1 Galaxy wrapper for samtools bam2fq
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2 ====================================
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3
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4 This wrapper is copyright 2014 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 This is a wrapper for part of the command line samtools suite.
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9
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10 This wrapper is available from the Galaxy Tool Shed at:
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11 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
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12
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13
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14 Automated Installation
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15 ======================
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16
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17 This should be straightforward, Galaxy should automatically download and install
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18 samtools if required.
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19
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20
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21 Manual Installation
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22 ===================
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23
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24 This expects samtools to be on the $PATH, and was tested using v0.1.19.
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25
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26 To install the wrapper copy or move the following files under the Galaxy tools
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27 folder, e.g. in a ``tools/samtools_bam2fq`` folder:
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28
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29 * ``samtools_bam2fq.xml`` (the Galaxy tool definition)
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30 * ``README.rst`` (this file)
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31
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32 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
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33 the tool. Just add the line, perhaps under the NGS tools section::
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34
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35 <tool file="samtools_bam2fq/samtools_bam2fq.xml" />
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36
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37 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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38 under Galaxy's ``test-data/`` folder. Then::
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39
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40 $ ./run_tests.sh -id samtools_bam2fq
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41
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42 That's it.
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43
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44
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45 History
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46 =======
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47
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48 ======= ======================================================================
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49 Version Changes
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50 ------- ----------------------------------------------------------------------
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51 v0.0.1 - Initial public release, tested with samtools v1.1.
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52 v0.0.2 - Defaults to pair-aware mode which requires pre-sorting by read name.
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53 ======= ======================================================================
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54
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55
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56 Developers
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57 ==========
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58
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59 Development is on this GitHub repository:
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60 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq
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61
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62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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63 the following command from the Galaxy root folder::
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64
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65 $ tar -czf samtools_bam2fq.tar.gz tools/samtools_bam2fq/README.rst tools/samtools_bam2fq/samtools_bam2fq.xml tools/samtools_bam2fq/tool_dependencies.xml test-data/sam_spec_padded.bam test-data/sam_spec_padded.sam test-data/sam_spec_padded.depad.bam test-data/sam_spec_padded.bam2fq.fastq test-data/sam_spec_padded.bam2fq_no_suf.fastq test-data/sam_spec_padded.bam2fq_singles.fastq test-data/sam_spec_padded.bam2fq_pairs.fastq
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66
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67 Check this worked::
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68
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69 $ tar -tzf samtools_bam2fq.tar.gz
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70 tools/samtools_bam2fq/README.rst
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71 tools/samtools_bam2fq/samtools_bam2fq.xml
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72 tools/samtools_bam2fq/tool_dependencies.xml
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73 test-data/sam_spec_padded.bam
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74 test-data/sam_spec_padded.sam
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75 test-data/sam_spec_padded.depad.bam
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76 test-data/sam_spec_padded.bam2fq.fastq
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77 test-data/sam_spec_padded.bam2fq_no_suf.fastq
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78 test-data/sam_spec_padded.bam2fq_singles.fastq
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79 test-data/sam_spec_padded.bam2fq_pairs.fastq
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80
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81
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82 Licence (MIT)
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83 =============
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84
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85 Permission is hereby granted, free of charge, to any person obtaining a copy
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86 of this software and associated documentation files (the "Software"), to deal
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87 in the Software without restriction, including without limitation the rights
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88 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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89 copies of the Software, and to permit persons to whom the Software is
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90 furnished to do so, subject to the following conditions:
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91
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92 The above copyright notice and this permission notice shall be included in
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93 all copies or substantial portions of the Software.
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94
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95 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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96 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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97 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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98 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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99 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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100 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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101 THE SOFTWARE.
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102
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103 NOTE: This is the licence for the Galaxy Wrapper only.
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104 samtools is available and licenced separately.
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