Mercurial > repos > peterjc > sample_seqs
comparison tools/sample_seqs/README.rst @ 0:3a807e5ea6c8 draft
Uploaded v0.0.1
author | peterjc |
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date | Thu, 27 Mar 2014 09:40:53 -0400 |
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children | 16ecf25d521f |
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1 Galaxy tool to find ORFs or simple CDSs | |
2 ======================================= | |
3 | |
4 This tool is copyright 2014 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) | |
9 to sub-sample sequence files (in a range of formats including FASTA, FASTQ, | |
10 and SFF). This can be useful for preparing a small sample of data to test | |
11 or time a new pipeline, or for reducing the read coverage in a de novo | |
12 assembly. | |
13 | |
14 This tool is available from the Galaxy Tool Shed at: | |
15 | |
16 * http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs | |
17 | |
18 | |
19 Automated Installation | |
20 ====================== | |
21 | |
22 This should be straightforward using the Galaxy Tool Shed, which should be | |
23 able to automatically install the dependency on Biopython, and then install | |
24 this tool and run its unit tests. | |
25 | |
26 | |
27 Manual Installation | |
28 =================== | |
29 | |
30 There are just two files to install to use this tool from within Galaxy: | |
31 | |
32 * ``sample_seqs.py`` (the Python script) | |
33 * ``sample_seqs.xml`` (the Galaxy tool definition) | |
34 | |
35 The suggested location is in a dedicated ``tools/sample_seqs`` folder. | |
36 | |
37 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the | |
38 tool. One suggested location is in the filters section. Simply add the line:: | |
39 | |
40 <tool file="sample_seqs/sample_seqs.xml" /> | |
41 | |
42 You will also need to install Biopython 1.62 or later. If you want to run | |
43 the unit tests, include this line in ``tools_conf.xml.sample`` and the sample | |
44 FASTA files under the ``test-data`` directory. Then:: | |
45 | |
46 ./run_functional_tests.sh -id sample_seqs | |
47 | |
48 That's it. | |
49 | |
50 | |
51 History | |
52 ======= | |
53 | |
54 ======= ====================================================================== | |
55 Version Changes | |
56 ------- ---------------------------------------------------------------------- | |
57 v0.0.1 - Initial version. | |
58 ======= ====================================================================== | |
59 | |
60 | |
61 Developers | |
62 ========== | |
63 | |
64 This script and related tools are being developed on this GitHub repository: | |
65 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs | |
66 | |
67 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
68 the following command from the Galaxy root folder:: | |
69 | |
70 $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff | |
71 | |
72 Check this worked:: | |
73 | |
74 $ tar -tzf sample_seqs.tar.gz | |
75 tools/sample_seqs/README.rst | |
76 tools/sample_seqs/sample_seqs.py | |
77 tools/sample_seqs/sample_seqs.xml | |
78 tools/sample_seqs/tool_dependencies.xml | |
79 test-data/ecoli.fastq | |
80 test-data/ecoli.sample_N100.fastq | |
81 test-data/get_orf_input.Suis_ORF.prot.fasta | |
82 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta | |
83 test-data/MID4_GLZRM4E04_rnd30_frclip.sff | |
84 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff | |
85 | |
86 | |
87 Licence (MIT) | |
88 ============= | |
89 | |
90 Permission is hereby granted, free of charge, to any person obtaining a copy | |
91 of this software and associated documentation files (the "Software"), to deal | |
92 in the Software without restriction, including without limitation the rights | |
93 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
94 copies of the Software, and to permit persons to whom the Software is | |
95 furnished to do so, subject to the following conditions: | |
96 | |
97 The above copyright notice and this permission notice shall be included in | |
98 all copies or substantial portions of the Software. | |
99 | |
100 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
101 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
102 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
103 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
104 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
105 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
106 THE SOFTWARE. |