Mercurial > repos > peterjc > samtools_depad
annotate tools/samtools_depad/README.rst @ 2:02572789ef6c draft
v0.0.4 Internal changes to command line handling
author | peterjc |
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date | Tue, 16 May 2017 09:29:05 -0400 |
parents | 01f8967ce1e0 |
children | 588c6ce25867 |
rev | line source |
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0 | 1 Galaxy wrapper for samtools depad |
2 ================================= | |
3 | |
2 | 4 This wrapper is copyright 2014-2017 by Peter Cock, The James Hutton Institute |
0 | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
6 See the licence text below. | |
7 | |
8 This is a wrapper for part of the command line samtools suite, v0.1.19 | |
9 | |
10 This wrapper is available from the Galaxy Tool Shed at: | |
2 | 11 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad |
0 | 12 |
13 | |
14 Automated Installation | |
15 ====================== | |
16 | |
17 This should be straightforward, Galaxy should automatically download and install | |
18 samtools 0.1.19 if required. | |
19 | |
20 | |
21 Manual Installation | |
22 =================== | |
23 | |
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24 This expects samtools to be on the ``$PATH``, and was tested using v0.1.19. |
0 | 25 |
26 To install the wrapper copy or move the following files under the Galaxy tools | |
27 folder, e.g. in a ``tools/samtools_depad`` folder: | |
28 | |
29 * ``samtools_depad.xml`` (the Galaxy tool definition) | |
30 * ``samtools_depad.py`` (the Python wrapper script) | |
31 * ``README.rst`` (this file) | |
32 | |
33 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
34 the tool. Just add the line, perhaps under the NGS tools section:: | |
35 | |
36 <tool file="samtools_depad/samtools_depad.xml" /> | |
37 | |
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38 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
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39 under Galaxy's ``test-data/`` folder. Then:: |
0 | 40 |
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41 $ ./run_tests.sh -id samtools_depad |
0 | 42 |
43 That's it. | |
44 | |
45 | |
46 History | |
47 ======= | |
48 | |
49 ======= ====================================================================== | |
50 Version Changes | |
51 ------- ---------------------------------------------------------------------- | |
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52 v0.0.1 - Initial public release. |
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53 v0.0.2 - Embed samtools citation in the tool XML. |
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54 - Removed unused imports from Python wrapper script. |
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55 v0.0.3 - Reorder XML elements (internal change only). |
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56 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
2 | 57 v0.0.4 - Use ``<command detect_errors="aggressive">`` (internal change only). |
58 - Single quote command line arguments (internal change only). | |
0 | 59 ======= ====================================================================== |
60 | |
61 | |
62 Developers | |
63 ========== | |
64 | |
65 Development is on this GitHub repository: | |
66 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad | |
67 | |
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68 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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69 Planemo commands (which requires you have set your Tool Shed access details in |
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70 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
0 | 71 |
2 | 72 $ planemo shed_update -t testtoolshed --check_diff tools/samtools_depad/ |
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73 ... |
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74 |
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75 or:: |
0 | 76 |
2 | 77 $ planemo shed_update -t toolshed --check_diff tools/samtools_depad/ |
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78 ... |
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79 |
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80 To just build and check the tar ball, use:: |
0 | 81 |
2 | 82 $ planemo shed_upload --tar_only tools/samtools_depad/ |
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83 ... |
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84 $ tar -tzf shed_upload.tar.gz |
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85 test-data/sam_spec_padded.bam |
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86 test-data/sam_spec_padded.depad.bam |
0 | 87 test-data/sam_spec_padded.fasta |
88 test-data/sam_spec_padded.sam | |
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89 tools/samtools_depad/README.rst |
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90 tools/samtools_depad/samtools_depad.py |
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91 tools/samtools_depad/samtools_depad.xml |
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92 tools/samtools_depad/tool_dependencies.xml |
0 | 93 |
94 | |
95 Licence (MIT) | |
96 ============= | |
97 | |
98 Permission is hereby granted, free of charge, to any person obtaining a copy | |
99 of this software and associated documentation files (the "Software"), to deal | |
100 in the Software without restriction, including without limitation the rights | |
101 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
102 copies of the Software, and to permit persons to whom the Software is | |
103 furnished to do so, subject to the following conditions: | |
104 | |
105 The above copyright notice and this permission notice shall be included in | |
106 all copies or substantial portions of the Software. | |
107 | |
108 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
109 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
110 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
111 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
112 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
113 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
114 THE SOFTWARE. | |
115 | |
116 NOTE: This is the licence for the Galaxy Wrapper only. | |
117 samtools is available and licenced separately. |