Mercurial > repos > peterjc > get_orfs_or_cdss
annotate tools/get_orfs_or_cdss/README.rst @ 6:64e67f172188 draft
Uploaded v0.0.6, corrected automated dependency definition
author | peterjc |
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date | Thu, 21 Nov 2013 10:47:53 -0500 |
parents | 5208c15805ec |
children | 705a2e2df7fb |
rev | line source |
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5 | 1 Galaxy tool to find ORFs or simple CDSs |
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 Biopython library functions) | |
9 to search nucleotide sequences for open reading frames (ORFs) or coding | |
10 sequences (CDSs) where the first potential start codon is used. See the | |
11 help text in the XML file for more information. | |
12 | |
13 This tool is available from the Galaxy Tool Shed at: | |
14 | |
15 * http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss | |
16 | |
17 See also the EMBOSS tool ``getorf`` which offers similar functionality and | |
18 has also been wrapped for use within Galaxy. | |
19 | |
20 | |
21 Automated Installation | |
22 ====================== | |
23 | |
24 This should be straightforward using the Galaxy Tool Shed, which should be | |
25 able to automatically install the dependency on Biopython, and then install | |
26 this tool and run its unit tests. | |
27 | |
28 | |
29 Manual Installation | |
30 =================== | |
31 | |
32 There are just two files to install to use this tool from within Galaxy: | |
33 | |
34 * get_orfs_or_cdss.py (the Python script) | |
35 * get_orfs_or_cdss.xml (the Galaxy tool definition) | |
36 | |
37 The suggested location is in a dedicated tools/get_orfs_or_cdss folder. | |
38 | |
39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
40 tool. One suggested location is in the filters section. Simply add the line:: | |
41 | |
42 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" /> | |
43 | |
44 You will also need to install Biopython 1.54 or later. If you want to run | |
45 the unit tests, include this line in tools_conf.xml.sample and the sample | |
46 FASTA files under the test-data directory. Then:: | |
47 | |
48 ./run_functional_tests.sh -id get_orfs_or_cdss | |
49 | |
50 That's it. | |
51 | |
52 | |
53 History | |
54 ======= | |
55 | |
56 ======= ====================================================================== | |
57 Version Changes | |
58 ------- ---------------------------------------------------------------------- | |
59 v0.0.1 - Initial version. | |
60 v0.0.2 - Correct labelling issue on reverse strand. | |
61 - Use the new <stdio> settings in the XML wrappers to catch errors | |
62 v0.0.3 - Include unit tests. | |
63 - Record Python script version when run from Galaxy. | |
64 v0.0.4 - Link to Tool Shed added to help text and this documentation. | |
65 v0.0.5 - Automated intallation of the Biopython dependency. | |
66 - Use reStructuredText for this README file. | |
67 - Adopt standard MIT License. | |
68 - Updated citation information (Cock et al. 2013). | |
69 - Renamed folder and adopted README.rst naming. | |
6
64e67f172188
Uploaded v0.0.6, corrected automated dependency definition
peterjc
parents:
5
diff
changeset
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70 v0.0.6 - Corrected automated dependency defintion. |
5 | 71 ======= ====================================================================== |
72 | |
73 | |
74 Developers | |
75 ========== | |
76 | |
77 This script and related tools were initially developed on the following hg branch: | |
78 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
79 | |
80 Development has now moved to a dedicated GitHub repository: | |
81 https://github.com/peterjc/pico_galaxy/tree/master/tools | |
82 | |
83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
84 the following command from the Galaxy root folder:: | |
85 | |
6
64e67f172188
Uploaded v0.0.6, corrected automated dependency definition
peterjc
parents:
5
diff
changeset
|
86 $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta |
5 | 87 |
88 Check this worked:: | |
89 | |
90 $ tar -tzf get_orfs_or_cdss.tar.gz | |
91 tools/get_orfs_or_cdss/README.rst | |
92 tools/get_orfs_or_cdss/get_orfs_or_cdss.py | |
93 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml | |
6
64e67f172188
Uploaded v0.0.6, corrected automated dependency definition
peterjc
parents:
5
diff
changeset
|
94 tools/get_orfs_or_cdss/tool_dependencies.xml |
5 | 95 test-data/get_orf_input.fasta |
96 test-data/get_orf_input.Suis_ORF.nuc.fasta | |
97 test-data/get_orf_input.Suis_ORF.prot.fasta | |
98 test-data/get_orf_input.t11_nuc_out.fasta | |
99 test-data/get_orf_input.t11_open_nuc_out.fasta | |
100 test-data/get_orf_input.t11_open_prot_out.fasta | |
101 test-data/get_orf_input.t11_prot_out.fasta | |
102 test-data/get_orf_input.t1_nuc_out.fasta | |
103 test-data/get_orf_input.t1_prot_out.fasta | |
104 test-data/Ssuis.fasta | |
105 | |
106 | |
107 Licence (MIT) | |
108 ============= | |
109 | |
110 Permission is hereby granted, free of charge, to any person obtaining a copy | |
111 of this software and associated documentation files (the "Software"), to deal | |
112 in the Software without restriction, including without limitation the rights | |
113 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
114 copies of the Software, and to permit persons to whom the Software is | |
115 furnished to do so, subject to the following conditions: | |
116 | |
117 The above copyright notice and this permission notice shall be included in | |
118 all copies or substantial portions of the Software. | |
119 | |
120 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
121 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
122 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
123 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
124 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
125 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
126 THE SOFTWARE. |