Mercurial > repos > jasper > align_back_trans
comparison tools/align_back_trans/README.rst @ 0:6c6b16cab42a draft
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author | jasper |
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date | Tue, 09 May 2017 13:22:02 -0400 |
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1 Galaxy tool to back-translate a protein alignment to nucleotides | |
2 ================================================================ | |
3 | |
4 This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below (MIT licence). | |
7 | |
8 This tool is a short Python script (using Biopython library functions) to | |
9 load a protein alignment, and matching nucleotide FASTA file of unaligned | |
10 sequences, which are threaded onto the protein alignment in order to produce | |
11 a codon aware nucleotide alignment - which can be viewed as a back translation. | |
12 | |
13 This tool is available from the Galaxy Tool Shed at: | |
14 | |
15 * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans | |
16 | |
17 The underlying Python script can also be used outside of Galaxy, for | |
18 details run:: | |
19 | |
20 $ python align_back_trans.py | |
21 | |
22 Automated Installation | |
23 ====================== | |
24 | |
25 This should be straightforward using the Galaxy Tool Shed, which should be | |
26 able to automatically install the dependency on Biopython, and then install | |
27 this tool and run its unit tests. | |
28 | |
29 | |
30 Manual Installation | |
31 =================== | |
32 | |
33 There are just two files to install to use this tool from within Galaxy: | |
34 | |
35 * ``align_back_trans.py`` (the Python script) | |
36 * ``align_back_trans.xml`` (the Galaxy tool definition) | |
37 | |
38 The suggested location is in a dedicated ``tools/align_back_trans`` folder. | |
39 | |
40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
41 the tool. One suggested location is in the multiple alignments section. Simply | |
42 add the line:: | |
43 | |
44 <tool file="align_back_trans/align_back_trans.xml" /> | |
45 | |
46 You will also need to install Biopython 1.62 or later. | |
47 | |
48 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
49 under Galaxy's ``test-data/`` folder. Then:: | |
50 | |
51 ./run_tests.sh -id align_back_trans | |
52 | |
53 That's it. | |
54 | |
55 | |
56 History | |
57 ======= | |
58 | |
59 ======= ====================================================================== | |
60 Version Changes | |
61 ------- ---------------------------------------------------------------------- | |
62 v0.0.1 - Initial version, based on a previously written Python script | |
63 v0.0.2 - Optionally check the translation is consistent | |
64 v0.0.3 - First official release | |
65 v0.0.4 - Simplified XML to apply input format to output data. | |
66 - Fixed error message when sequence length not a multiple of three. | |
67 v0.0.5 - More explicit error messages when seqences lengths do not match. | |
68 - Tool definition now embeds citation information. | |
69 v0.0.6 - Reorder XML elements (internal change only). | |
70 - Use ``format_source=...`` tag. | |
71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
72 v0.0.7 - Minor Python code style improvements (internal change only). | |
73 ======= ====================================================================== | |
74 | |
75 | |
76 Developers | |
77 ========== | |
78 | |
79 This script was initially developed on this repository: | |
80 https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py | |
81 | |
82 With the addition of a Galaxy wrapper, developement moved here: | |
83 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans | |
84 | |
85 For pushing a release to the test or main "Galaxy Tool Shed", use the following | |
86 Planemo commands (which requires you have set your Tool Shed access details in | |
87 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
88 | |
89 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ | |
90 ... | |
91 | |
92 or:: | |
93 | |
94 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/ | |
95 ... | |
96 | |
97 To just build and check the tar ball, use:: | |
98 | |
99 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/align_back_trans/ | |
100 ... | |
101 $ tar -tzf shed_upload.tar.gz | |
102 test-data/demo_nucs.fasta | |
103 test-data/demo_nucs_trailing_stop.fasta | |
104 test-data/demo_prot_align.fasta | |
105 test-data/demo_nuc_align.fasta | |
106 tools/align_back_trans/README.rst | |
107 tools/align_back_trans/align_back_trans.py | |
108 tools/align_back_trans/align_back_trans.xml | |
109 tools/align_back_trans/tool_dependencies.xml | |
110 | |
111 | |
112 Licence (MIT) | |
113 ============= | |
114 | |
115 Permission is hereby granted, free of charge, to any person obtaining a copy | |
116 of this software and associated documentation files (the "Software"), to deal | |
117 in the Software without restriction, including without limitation the rights | |
118 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
119 copies of the Software, and to permit persons to whom the Software is | |
120 furnished to do so, subject to the following conditions: | |
121 | |
122 The above copyright notice and this permission notice shall be included in | |
123 all copies or substantial portions of the Software. | |
124 | |
125 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
126 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
127 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
128 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
129 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
130 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
131 THE SOFTWARE. |