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annotate README.rst @ 15:367a0403b7d2 draft

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author peterjc
date Thu, 07 May 2015 05:43:50 -0400
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1 Galaxy tool to draw a Venn Diagram with up to 3 sets
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2 ====================================================
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4 This tool is copyright 2011-2015 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.
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8 This tool is a short Python script (using both the Galaxy and Biopython library
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9 functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
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10 sets, which are then drawn using the R limma package function vennDiagram
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11 (called from Python using rpy).
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13 This tool is available from the Galaxy Tool Shed at:
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14 http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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17 Automated Installation
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18 ======================
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20 This should be straightforward, Galaxy should automatically download the tool
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21 and the Biopython dependency.
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23 You will still need to install the R/Bioconductor package limma.
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26 Manual Installation
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27 ===================
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29 There are just two files to install:
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31 * ``venn_list.py`` (the Python script)
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32 * ``venn_list.xml`` (the Galaxy tool definition)
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34 The suggested location is in the Galaxy folder ``tools/plotting`` next to other
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35 graph drawing tools, or a dedicated ``tools/venn_list`` directory.
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37 You will also need to install Biopython 1.54 or later, and the R/Bioconductor
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38 package limma. You should already have rpy installed for other Galaxy tools.
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40 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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41 tool. The suggested location is in the "Graph/Display Data" section. Simply add
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42 the line::
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44 <tool file="venn_list/venn_list.xml" />
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46 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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47 under Galaxy's ``test-data/`` folder. Then::
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49 ./run_tests.sh -id venn_list
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52 History
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53 =======
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55 ======= ======================================================================
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56 Version Changes
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57 ------- ----------------------------------------------------------------------
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58 v0.0.3 - Initial public release.
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59 v0.0.4 - Ignore blank lines when loading IDs from tabular files
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60 v0.0.5 - Explicit Galaxy error handling of return codes
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61 v0.0.6 - Added unit tests.
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62 - Use reStructuredText for this README file.
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63 - Adopt standard MIT licence.
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64 - Updated citation information (Cock et al. 2013).
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65 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
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66 v0.0.7 - Renamed folder and README file.
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67 - Tool definition now embeds citation information.
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68 v0.0.8 - Reorder XML elements (internal change only).
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69 - Fixed and improved error handling when rpy is not available.
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70 - Test output relaxed to cope with more variation in PDF output.
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71 - Declare Biopython dependency via the Tool Shed.
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72 ======= ======================================================================
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75 Developers
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76 ==========
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78 This script and related tools were initially developed on the following hg branch:
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79 http://bitbucket.org/peterjc/galaxy-central/src/tools
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81 Development has now moved to a dedicated GitHub repository:
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82 https://github.com/peterjc/pico_galaxy
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84 For pushing a release to the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/
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85 use the following Planemo command (which requires you have set your Tool Shed
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86 access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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88 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/
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89 ...
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90 $ tar -tzf shed_upload.tar.gz
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91 README.rst
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92 test-data/magic.pdf
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93 test-data/rhodopsin_proteins.fasta
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94 test-data/venn_list.tabular
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95 tool_dependencies.xml
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96 venn_list.py
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97 venn_list.xml
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98
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99 This tar-ball can be uploaded to the Tool Shed via the web interface (using
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100 the ``--tar`` command or via
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101 Planemo. More simply, the following single command can be used:
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102
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103 $ planemo shed_upload
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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.