Mercurial > repos > peterjc > seq_primer_clip
comparison tools/seq_primer_clip/README.rst @ 2:ee5acea162a7 draft
Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency
author | peterjc |
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date | Thu, 24 Oct 2013 09:37:25 -0400 |
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children | 708ce1e5ac94 |
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1 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads | |
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 (MIT licence). | |
7 | |
8 This tool is a short Python script (using the Galaxy library functions and | |
9 Biopython). It is available from the Galaxy Tool Shed here: | |
10 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip | |
11 | |
12 | |
13 Automated Installation | |
14 ====================== | |
15 | |
16 This should be straightforward using the Galaxy Tool Shed, which should be | |
17 able to automatically install the dependency on Biopython, and then install | |
18 this tool and run its unit tests. | |
19 | |
20 | |
21 Manual Installation | |
22 =================== | |
23 | |
24 There are just two files to install: | |
25 | |
26 * seq_primer_clip.py (the Python script) | |
27 * seq_primer_clip.xml (the Galaxy tool definition) | |
28 | |
29 The suggested location is a new tools/seq_primer_clip folder. You will also | |
30 need to modify the tools_conf.xml file to tell Galaxy to offer the tool:: | |
31 | |
32 <tool file="seq_primer_clip/seq_primer_clip.xml" /> | |
33 | |
34 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
35 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
36 | |
37 $ ./run_functional_tests.sh -id seq_primer_clip | |
38 | |
39 You will also need to install Biopython 1.54 or later. That's it. | |
40 | |
41 | |
42 History | |
43 ======= | |
44 | |
45 ======= ====================================================================== | |
46 Version Changes | |
47 ------- ---------------------------------------------------------------------- | |
48 v0.0.1 - Initial version (not publicly released) | |
49 v0.0.2 - Sort primers by length (longest and therefore most specific first) | |
50 v0.0.3 - Consider missing bases at start/end of read as mismatches | |
51 v0.0.4 - Apply minimum length to sequences with no match too | |
52 v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes | |
53 v0.0.6 - Added some functional tests | |
54 v0.0.7 - Added error check for bad filename arguments | |
55 v0.0.8 - Record version of Python script when run from Galaxy. | |
56 - Check for errors using Python script's return code. | |
57 v0.0.9 - Moved test data to workaround Galaxy Tool Shed limititation. | |
58 v0.0.10 - Include links to Tool Shed in help text and this README file. | |
59 - Use reStructuredText for this README file. | |
60 - Adopted standard MIT licence. | |
61 - Automated installation of Biopython dependency. | |
62 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy | |
63 - Renamed folder and adopted README.rst naming. | |
64 ======= ====================================================================== | |
65 | |
66 | |
67 Developers | |
68 ========== | |
69 | |
70 This script and related tools were initially developed on the following hg branches: | |
71 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter | |
72 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
73 | |
74 Development has now moved to a dedicated GitHub repository: | |
75 https://github.com/peterjc/pico_galaxy | |
76 | |
77 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
78 the following command from the Galaxy root folder:: | |
79 | |
80 $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/repository_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* | |
81 | |
82 Check this worked:: | |
83 | |
84 $ tar -tzf seq_primer_clip.tar.gz | |
85 tools/seq_primer_clip/README.rst | |
86 tools/seq_primer_clip/seq_primer_clip.xml | |
87 tools/seq_primer_clip/seq_primer_clip.py | |
88 tools/seq_primer_clip/repository_dependencies.xml | |
89 test-data/dop_primers.fasta | |
90 test-data/MID4_GLZRM4E04_rnd30.fasta | |
91 test-data/MID4_GLZRM4E04_rnd30.fastqsanger | |
92 test-data/MID4_GLZRM4E04_rnd30_fclip.fasta | |
93 test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger | |
94 test-data/MID4_GLZRM4E04_rnd30_fclip.sff | |
95 test-data/MID4_GLZRM4E04_rnd30_frclip.fasta | |
96 test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger | |
97 test-data/MID4_GLZRM4E04_rnd30_frclip.sff | |
98 test-data/MID4_GLZRM4E04_rnd30.sff | |
99 | |
100 | |
101 Licence (MIT) | |
102 ============= | |
103 | |
104 Permission is hereby granted, free of charge, to any person obtaining a copy | |
105 of this software and associated documentation files (the "Software"), to deal | |
106 in the Software without restriction, including without limitation the rights | |
107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
108 copies of the Software, and to permit persons to whom the Software is | |
109 furnished to do so, subject to the following conditions: | |
110 | |
111 The above copyright notice and this permission notice shall be included in | |
112 all copies or substantial portions of the Software. | |
113 | |
114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
120 THE SOFTWARE. |