Mercurial > repos > peterjc > samtools_idxstats
annotate tools/samtools_idxstats/README.rst @ 2:71afa65f444a draft default tip
v0.0.5 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 09:24:18 -0400 |
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1 Galaxy wrapper for samtools idxstats |
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2 ==================================== |
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3 |
1 | 4 This wrapper is copyright 2013-2015 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, v0.1.19 |
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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_idxstats |
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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 0.1.19 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_idxstats`` folder: |
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28 |
1 | 29 * ``samtools_idxstats.xml`` (the Galaxy tool definition) |
30 * ``samtools_idxstats.py`` (the Python wrapper script) | |
31 * ``README.rst`` (this file) | |
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32 |
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33 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer |
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34 the tool. Just add the line, perhaps under the NGS tools section:: |
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35 |
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36 <tool file="samtools_idxstats/samtools_idxstats.xml" /> |
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37 |
1 | 38 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
39 under Galaxy's ``test-data/`` folder. Then:: | |
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40 |
1 | 41 $ ./run_tests.sh -id samtools_idxstats |
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42 |
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43 That's it. |
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44 |
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45 |
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46 History |
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47 ======= |
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48 |
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49 ======= ====================================================================== |
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50 Version Changes |
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51 ------- ---------------------------------------------------------------------- |
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52 v0.0.1 - Initial public release |
1 | 53 v0.0.2 - Use quoted filenames when calling samtools (in case of spaces etc) |
54 v0.0.3 - Embed samtools citation in tool XML. | |
55 v0.0.4 - Reorder XML elements (internal change only). | |
56 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
2 | 57 v0.0.5 - Use ``<command detect_errors="aggressive">`` (internal change only). |
58 - Single quote command line arguments (internal change only). | |
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59 ======= ====================================================================== |
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60 |
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61 |
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62 Developers |
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63 ========== |
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64 |
1 | 65 Development is on this GitHub repository: |
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66 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats |
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67 |
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68 |
1 | 69 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
70 Planemo commands (which requires you have set your Tool Shed access details in | |
71 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
72 | |
2 | 73 $ planemo shed_update -t testtoolshed --check_diff tools/samtools_idxstats/ |
1 | 74 ... |
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75 |
1 | 76 or:: |
77 | |
2 | 78 $ planemo shed_update -t toolshed --check_diff tools/samtools_idxstats/ |
1 | 79 ... |
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80 |
1 | 81 To just build and check the tar ball, use:: |
82 | |
2 | 83 $ planemo shed_upload --tar_only tools/samtools_idxstats/ |
1 | 84 ... |
85 $ tar -tzf shed_upload.tar.gz | |
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86 test-data/ex1.bam |
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87 test-data/ex1.idxstats.tabular |
1 | 88 tools/samtools_idxstats/README.rst |
89 tools/samtools_idxstats/samtools_idxstats.py | |
90 tools/samtools_idxstats/samtools_idxstats.xml | |
91 tools/samtools_idxstats/tool_dependencies.xml | |
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92 |
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93 |
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94 Licence (MIT) |
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95 ============= |
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96 |
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97 Permission is hereby granted, free of charge, to any person obtaining a copy |
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98 of this software and associated documentation files (the "Software"), to deal |
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99 in the Software without restriction, including without limitation the rights |
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100 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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101 copies of the Software, and to permit persons to whom the Software is |
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102 furnished to do so, subject to the following conditions: |
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103 |
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104 The above copyright notice and this permission notice shall be included in |
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105 all copies or substantial portions of the Software. |
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106 |
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107 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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108 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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109 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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110 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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111 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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112 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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113 THE SOFTWARE. |
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114 |
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115 NOTE: This is the licence for the Galaxy Wrapper only. |
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116 samtools is available and licenced separately. |