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1 Galaxy tool reporting sequence composition
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2 ==========================================
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3
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4 This tool is copyright 2014-2017 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) to
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9 loop over given sequence files (in a range of formats including FASTA, FASTQ,
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10 and SFF), and report the count of each letter (i.e. amino acids or bases).
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11
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12 This can be useful for sanity checking assemblies (e.g. proportion of N
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13 bases) or looking at differences in base composition.
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14
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15 This tool is available from the Galaxy Tool Shed at:
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16
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17 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_composition
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18
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19
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20 Automated Installation
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21 ======================
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22
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23 This should be straightforward using the Galaxy Tool Shed, which should be
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24 able to automatically install the dependency on Biopython, and then install
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25 this tool and run its unit tests.
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26
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27
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28 Manual Installation
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29 ===================
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30
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31 There are just two files to install to use this tool from within Galaxy:
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32
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33 * ``seq_composition.py`` (the Python script)
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34 * ``seq_composition.xml`` (the Galaxy tool definition)
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35
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36 The suggested location is in a dedicated ``tools/seq_composition`` folder.
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37
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38 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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39 tool. One suggested location is in the filters section. Simply add the line::
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40
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41 <tool file="seq_composition/seq_composition.xml" />
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42
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43 You will also need to install Biopython 1.62 or later.
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44
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45 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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46 under Galaxy's ``test-data/`` folder. Then::
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47
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48 ./run_tests.sh -id seq_composition
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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 - Tool definition now embeds citation information.
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61 v0.0.2 - Reorder XML elements (internal change only).
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62 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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63 v0.0.3 - Python style updates (internal change only).
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64 ======= ======================================================================
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65
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66
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67 Developers
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68 ==========
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69
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70 This script and related tools are being developed on this GitHub repository:
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71 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition
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72
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73
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74 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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75 Planemo commands (which requires you have set your Tool Shed access details in
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76 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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77
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78 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/
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79 ...
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80
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81 or::
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82
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83 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/
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84 ...
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85
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86 To just build and check the tar ball, use::
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87
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88 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_composition/
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89 ...
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90 $ tar -tzf shed_upload.tar.gz
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91 test-data/MID4_GLZRM4E04_rnd30_frclip.sff
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92 test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular
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93 test-data/ecoli.fastq
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94 test-data/ecoli.seq_composition.tabular
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95 test-data/four_human_proteins.fasta
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96 test-data/four_human_proteins.seq_composition.tabular
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97 tools/seq_composition/README.rst
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98 tools/seq_composition/seq_composition.py
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99 tools/seq_composition/seq_composition.xml
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100 tools/seq_composition/tool_dependencies.xml
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101
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102
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103 Licence (MIT)
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104 =============
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105
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106 Permission is hereby granted, free of charge, to any person obtaining a copy
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107 of this software and associated documentation files (the "Software"), to deal
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108 in the Software without restriction, including without limitation the rights
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109 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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110 copies of the Software, and to permit persons to whom the Software is
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111 furnished to do so, subject to the following conditions:
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112
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113 The above copyright notice and this permission notice shall be included in
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114 all copies or substantial portions of the Software.
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115
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116 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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117 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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118 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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119 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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120 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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121 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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122 THE SOFTWARE.
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