Mercurial > repos > peterjc > seq_rename
comparison tools/seq_rename/README.rst @ 2:7c0642fc57ad draft
Uploaded v0.0.4, automatic dependency on Biopython 1.62, new README file, citation information, MIT licence.
Includes additional tested added in v0.0.3
author | peterjc |
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date | Fri, 11 Oct 2013 04:39:16 -0400 |
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children | e1398f2ba9fe |
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1 Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences | |
2 ========================================================= | |
3 | |
4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 This tool is a short Python script (using Biopython library functions) to rename | |
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as | |
10 two columns of a tabular file. The output order follows that of the sequence file, | |
11 and if there are duplicates in the input sequence file, there will be duplicates | |
12 in the output sequence file. | |
13 | |
14 This tool is available from the Galaxy Tool Shed, | |
15 | |
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename | |
17 | |
18 See also the sister tools to filter or select sequence files according to IDs | |
19 from column(s) of tabular file: | |
20 | |
21 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
22 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id | |
23 | |
24 | |
25 Automated Installation | |
26 ====================== | |
27 | |
28 This should be straightforward using the Galaxy Tool Shed, which should be | |
29 able to automatically install the dependency on Biopython, and then install | |
30 this tool and run its unit tests. | |
31 | |
32 | |
33 Manual Installation | |
34 =================== | |
35 | |
36 There are just two files to install to use this tool from within Galaxy: | |
37 | |
38 * seq_rename.py (the Python script) | |
39 * seq_rename.xml (the Galaxy tool definition) | |
40 | |
41 The suggested location is in a dedicated tools/seq_rename folder. | |
42 | |
43 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
44 tool. One suggested location is in the filters section. Simply add the line:: | |
45 | |
46 <tool file="seq_rename/seq_rename.xml" /> | |
47 | |
48 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
49 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
50 | |
51 $ ./run_functional_tests.sh -id seq_rename | |
52 | |
53 You will also need to install Biopython 1.54 or later. That's it. | |
54 | |
55 | |
56 History | |
57 ======= | |
58 | |
59 ======= ====================================================================== | |
60 Version Changes | |
61 ------- ---------------------------------------------------------------------- | |
62 v0.0.1 - Initial version. | |
63 v0.0.2 - Record script version when run from Galaxy. | |
64 - Add unit test. | |
65 - Check for errors using Python script's return code. | |
66 v0.0.3 - Link to Tool Shed added to help text and this documentation. | |
67 v0.0.4 - Automated installation of Biopython dependency. | |
68 - Use reStructuredText for this README file. | |
69 - Adopt standard MIT License. | |
70 - Updated citation information (Cock et al. 2013). | |
71 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy | |
72 - Renamed folder and adopted README.rst naming. | |
73 ======= ====================================================================== | |
74 | |
75 | |
76 Developers | |
77 ========== | |
78 | |
79 This script and related tools were initially developed on the following hg branch: | |
80 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
81 | |
82 Development has now moved to a dedicated GitHub repository: | |
83 https://github.com/peterjc/pico_galaxy/tree/master/tools | |
84 | |
85 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
86 the following command from the Galaxy root folder:: | |
87 | |
88 $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta | |
89 | |
90 Check this worked:: | |
91 | |
92 $ tar -tzf seq_rename.tar.gz | |
93 tools/seq_rename/README.rst | |
94 tools/seq_rename/seq_rename.py | |
95 tools/seq_rename/seq_rename.xml | |
96 tools/seq_rename/repository_dependencies.xml | |
97 test-data/four_human_proteins.fasta | |
98 test-data/four_human_proteins.rename.tabular | |
99 test-data/four_human_proteins.rename.fasta | |
100 | |
101 | |
102 Licence (MIT) | |
103 ============= | |
104 | |
105 Permission is hereby granted, free of charge, to any person obtaining a copy | |
106 of this software and associated documentation files (the "Software"), to deal | |
107 in the Software without restriction, including without limitation the rights | |
108 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
109 copies of the Software, and to permit persons to whom the Software is | |
110 furnished to do so, subject to the following conditions: | |
111 | |
112 The above copyright notice and this permission notice shall be included in | |
113 all copies or substantial portions of the Software. | |
114 | |
115 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
116 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
117 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
118 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
119 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
120 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
121 THE SOFTWARE. |