Mercurial > repos > peterjc > get_orfs_or_cdss
annotate tools/get_orfs_or_cdss/README.rst @ 7:705a2e2df7fb draft
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author | peterjc |
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date | Thu, 30 Jul 2015 12:35:31 -0400 |
parents | 64e67f172188 |
children | 09a8be9247ca |
rev | line source |
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5 | 1 Galaxy tool to find ORFs or simple CDSs |
2 ======================================= | |
3 | |
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4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute |
5 | 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 | |
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34 * ``get_orfs_or_cdss.py`` (the Python script) |
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35 * ``get_orfs_or_cdss.xml`` (the Galaxy tool definition) |
5 | 36 |
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37 The suggested location is in a dedicated ``tools/get_orfs_or_cdss`` folder. |
5 | 38 |
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39 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the |
5 | 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 | |
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44 You will also need to install Biopython 1.65 or later (slightly older versions |
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45 should be fine, but will not have the latest NCBI genetic code tables). |
5 | 46 |
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47 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
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48 under Galaxy's ``test-data/`` folder. Then:: |
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49 |
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50 ./run_tests.sh -id get_orfs_or_cdss |
5 | 51 |
52 That's it. | |
53 | |
54 | |
55 History | |
56 ======= | |
57 | |
58 ======= ====================================================================== | |
59 Version Changes | |
60 ------- ---------------------------------------------------------------------- | |
61 v0.0.1 - Initial version. | |
62 v0.0.2 - Correct labelling issue on reverse strand. | |
63 - Use the new <stdio> settings in the XML wrappers to catch errors | |
64 v0.0.3 - Include unit tests. | |
65 - Record Python script version when run from Galaxy. | |
66 v0.0.4 - Link to Tool Shed added to help text and this documentation. | |
67 v0.0.5 - Automated intallation of the Biopython dependency. | |
68 - Use reStructuredText for this README file. | |
69 - Adopt standard MIT License. | |
70 - Updated citation information (Cock et al. 2013). | |
71 - Renamed folder and adopted README.rst naming. | |
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72 v0.0.6 - Corrected automated dependency defintion. |
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73 v0.0.7 - Tool definition now embeds citation information. |
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74 v0.1.0 - Tool now outputs BED formatted calls (by @erasche, Eric Rasche). |
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75 - Using ``optparse`` for the Python command line API (Eric Rasche). |
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76 - Added NCBI genetic code table 24, Pterobranchia Mitochondrial. |
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77 v0.1.1 - Reorder XML elements (internal change only). |
5 | 78 ======= ====================================================================== |
79 | |
80 | |
81 Developers | |
82 ========== | |
83 | |
84 This script and related tools were initially developed on the following hg branch: | |
85 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
86 | |
87 Development has now moved to a dedicated GitHub repository: | |
88 https://github.com/peterjc/pico_galaxy/tree/master/tools | |
89 | |
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90 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
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91 Planemo commands (which requires you have set your Tool Shed access details in |
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92 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
5 | 93 |
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94 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ |
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95 ... |
5 | 96 |
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97 or:: |
5 | 98 |
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99 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ |
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100 ... |
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101 |
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102 To just build and check the tar ball, use:: |
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103 |
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104 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/ |
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105 ... |
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106 $ tar -tzf shed_upload.tar.gz |
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107 test-data/Ssuis.fasta |
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108 test-data/get_orf_input.Suis_ORF.bed |
5 | 109 test-data/get_orf_input.Suis_ORF.nuc.fasta |
110 test-data/get_orf_input.Suis_ORF.prot.fasta | |
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111 test-data/get_orf_input.fasta |
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112 test-data/get_orf_input.t11_bed_out.bed |
5 | 113 test-data/get_orf_input.t11_nuc_out.fasta |
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114 test-data/get_orf_input.t11_open_bed_out.bed |
5 | 115 test-data/get_orf_input.t11_open_nuc_out.fasta |
116 test-data/get_orf_input.t11_open_prot_out.fasta | |
117 test-data/get_orf_input.t11_prot_out.fasta | |
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118 test-data/get_orf_input.t1_bed_out.bed |
5 | 119 test-data/get_orf_input.t1_nuc_out.fasta |
120 test-data/get_orf_input.t1_prot_out.fasta | |
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121 tools/get_orfs_or_cdss/get_orfs_or_cdss.py |
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122 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
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123 tools/get_orfs_or_cdss/README.rst |
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124 tools/get_orfs_or_cdss/tool_dependencies.xml |
5 | 125 |
126 | |
127 Licence (MIT) | |
128 ============= | |
129 | |
130 Permission is hereby granted, free of charge, to any person obtaining a copy | |
131 of this software and associated documentation files (the "Software"), to deal | |
132 in the Software without restriction, including without limitation the rights | |
133 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
134 copies of the Software, and to permit persons to whom the Software is | |
135 furnished to do so, subject to the following conditions: | |
136 | |
137 The above copyright notice and this permission notice shall be included in | |
138 all copies or substantial portions of the Software. | |
139 | |
140 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
141 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
142 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
143 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
144 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
145 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
146 THE SOFTWARE. |