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5
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1 Galaxy tool to find ORFs or simple CDSs
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2 =======================================
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3
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4 This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below (MIT licence).
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7
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8 This tool is a short Python script (using Biopython library functions)
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9 to search nucleotide sequences for open reading frames (ORFs) or coding
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10 sequences (CDSs) where the first potential start codon is used. See the
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11 help text in the XML file for more information.
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12
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13 This tool is available from the Galaxy Tool Shed at:
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14
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15 * http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
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16
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17 See also the EMBOSS tool ``getorf`` which offers similar functionality and
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18 has also been wrapped for use within Galaxy.
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19
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20
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21 Automated Installation
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22 ======================
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23
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24 This should be straightforward using the Galaxy Tool Shed, which should be
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25 able to automatically install the dependency on Biopython, and then install
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26 this tool and run its unit tests.
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27
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28
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29 Manual Installation
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30 ===================
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31
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32 There are just two files to install to use this tool from within Galaxy:
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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)
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36
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37 The suggested location is in a dedicated tools/get_orfs_or_cdss folder.
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38
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39 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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40 tool. One suggested location is in the filters section. Simply add the line::
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41
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42 <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
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43
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44 You will also need to install Biopython 1.54 or later. If you want to run
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45 the unit tests, include this line in tools_conf.xml.sample and the sample
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46 FASTA files under the test-data directory. Then::
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47
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48 ./run_functional_tests.sh -id get_orfs_or_cdss
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49
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50 That's it.
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51
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52
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53 History
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54 =======
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55
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56 ======= ======================================================================
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57 Version Changes
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58 ------- ----------------------------------------------------------------------
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59 v0.0.1 - Initial version.
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60 v0.0.2 - Correct labelling issue on reverse strand.
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61 - Use the new <stdio> settings in the XML wrappers to catch errors
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62 v0.0.3 - Include unit tests.
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63 - Record Python script version when run from Galaxy.
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64 v0.0.4 - Link to Tool Shed added to help text and this documentation.
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65 v0.0.5 - Automated intallation of the Biopython dependency.
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66 - Use reStructuredText for this README file.
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67 - Adopt standard MIT License.
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68 - Updated citation information (Cock et al. 2013).
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69 - Renamed folder and adopted README.rst naming.
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70 ======= ======================================================================
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71
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72
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73 Developers
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74 ==========
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75
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76 This script and related tools were initially developed on the following hg branch:
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77 http://bitbucket.org/peterjc/galaxy-central/src/tools
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78
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79 Development has now moved to a dedicated GitHub repository:
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80 https://github.com/peterjc/pico_galaxy/tree/master/tools
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81
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82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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83 the following command from the Galaxy root folder::
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84
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85 $ 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/repository_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta
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86
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87 Check this worked::
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88
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89 $ tar -tzf get_orfs_or_cdss.tar.gz
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90 tools/get_orfs_or_cdss/README.rst
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91 tools/get_orfs_or_cdss/get_orfs_or_cdss.py
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92 tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
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93 tools/get_orfs_or_cdss/repository_dependencies.xml
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94 test-data/get_orf_input.fasta
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95 test-data/get_orf_input.Suis_ORF.nuc.fasta
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96 test-data/get_orf_input.Suis_ORF.prot.fasta
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97 test-data/get_orf_input.t11_nuc_out.fasta
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98 test-data/get_orf_input.t11_open_nuc_out.fasta
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99 test-data/get_orf_input.t11_open_prot_out.fasta
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100 test-data/get_orf_input.t11_prot_out.fasta
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101 test-data/get_orf_input.t1_nuc_out.fasta
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102 test-data/get_orf_input.t1_prot_out.fasta
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103 test-data/Ssuis.fasta
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104
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105
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106 Licence (MIT)
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107 =============
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108
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109 Permission is hereby granted, free of charge, to any person obtaining a copy
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110 of this software and associated documentation files (the "Software"), to deal
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111 in the Software without restriction, including without limitation the rights
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112 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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113 copies of the Software, and to permit persons to whom the Software is
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114 furnished to do so, subject to the following conditions:
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115
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116 The above copyright notice and this permission notice shall be included in
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117 all copies or substantial portions of the Software.
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118
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119 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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120 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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121 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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122 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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123 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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124 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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125 THE SOFTWARE.
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