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4
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1 BAM coverage statistics using samtools idxstats and depth
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2 =========================================================
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3
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4 This tool is copyright 2014-2017 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 Internally this tool uses the command-line samtools suite.
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9
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10 This tool is available from the Galaxy Tool Shed at:
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11 http://toolshed.g2.bx.psu.edu/view/peterjc/coverage_stats
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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, provided your Galaxy is setup to use Conda and
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18 BioConda for dependencies - Galaxy should then automatically download and
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19 install the expected version of samtools.
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20
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21
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22 Manual Installation
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23 ===================
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24
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25 This expects samtools to be on the ``$PATH``, and was tested using v1.3.1.
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26
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27 To install the wrapper copy or move the following files under the Galaxy tools
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28 folder, e.g. in a ``tools/coverage_stats`` folder:
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29
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30 * ``coverage_stats.xml`` (the Galaxy tool definition)
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31 * ``coverage_stats.py`` (the Python wrapper script)
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32 * ``README.rst`` (this file)
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33
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34 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
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35 the tool. Just add the line, perhaps under the NGS tools section::
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36
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37 <tool file="coverage_stats/coverage_stats.xml" />
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38
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39 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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40 under Galaxy's ``test-data/`` folder. Then::
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41
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42 $ ./run_tests.sh -id coverage_stats
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43
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44 That's it.
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45
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46
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47 History
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48 =======
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49
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50 ======= ======================================================================
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51 Version Changes
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52 ------- ----------------------------------------------------------------------
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53 v0.0.1 - Initial public release
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54 v0.0.2 - Cope with samtools' default depth limit using modified samtools,
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55 see https://github.com/samtools/samtools/pull/322
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56 v0.0.3 - Cope with no coverage in final contigs.
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57 v0.0.4 - Reorder XML elements (internal change only).
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58 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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59 v0.0.5 - Expose new ``samtools depth -d ...`` argument added in samtools v1.3
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60 - Depends on samtools v1.4.1 via Conda, which IS NOT AVAILABLE as a
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61 legacy Tool Shed package.
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62 - Apply the new maximum depth parameter within the script to ensure
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63 excess coverage is clear by getting the max coverage equal to the
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64 max depth setting (the raw output from samtools is more fuzzy).
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65 - Report total length and overall mean coverage in stdout.
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66 - Use ``<command detect_errors="aggressive">`` (internal change only).
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67 - Single quote command line arguments (internal change only).
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68 v0.0.6 - Python 3 compatibility fix.
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69 v0.1.0 - Provide proper command line API for the Python script.
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70 ======= ======================================================================
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71
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72
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73 Developers
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74 ==========
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75
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76 Development is on this GitHub repository:
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77 https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats
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78
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79 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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80 Planemo commands (which requires you have set your Tool Shed access details in
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81 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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82
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83 $ planemo shed_update -t testtoolshed --check_diff tools/coverage_stats/
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84 ...
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85
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86 or::
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87
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88 $ planemo shed_update -t toolshed --check_diff tools/coverage_stats/
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89 ...
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90
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91 To just build and check the tar ball, use::
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92
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93 $ planemo shed_upload --tar_only tools/coverage_stats/
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94 ...
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95 $ tar -tzf shed_upload.tar.gz
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96 tools/coverage_stats/README.rst
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97 tools/coverage_stats/coverage_stats.xml
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98 tools/coverage_stats/coverage_stats.py
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99 ...
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100
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101
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102 Licence (MIT)
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103 =============
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104
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105 Permission is hereby granted, free of charge, to any person obtaining a copy
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106 of this software and associated documentation files (the "Software"), to deal
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107 in the Software without restriction, including without limitation the rights
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108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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109 copies of the Software, and to permit persons to whom the Software is
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110 furnished to do so, subject to the following conditions:
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111
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112 The above copyright notice and this permission notice shall be included in
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113 all copies or substantial portions of the Software.
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114
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115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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121 THE SOFTWARE.
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122
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123 NOTE: This is the licence for the Galaxy Wrapper only.
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124 samtools is available and licenced separately.
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