Mercurial > repos > peterjc > venn_list
annotate tools/venn_list/README.rst @ 4:991342eca214 draft
Uploaded v0.0.8a, declare Biopython dependency via Tool Shed
author | peterjc |
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date | Wed, 29 Apr 2015 11:00:41 -0400 |
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children | 26e35d5133a1 |
rev | line source |
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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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3 |
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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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7 |
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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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12 |
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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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15 |
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16 |
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17 Automated Installation |
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18 ====================== |
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19 |
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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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22 |
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23 You will still need to install the R/Bioconductor package limma. |
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24 |
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25 |
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26 Manual Installation |
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27 =================== |
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28 |
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29 There are just two files to install: |
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30 |
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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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33 |
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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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36 |
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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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39 |
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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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43 |
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44 <tool file="venn_list/venn_list.xml" /> |
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45 |
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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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48 |
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49 ./run_tests.sh -id venn_list |
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50 |
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51 |
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52 History |
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53 ======= |
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54 |
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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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73 |
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74 |
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75 Developers |
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76 ========== |
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77 |
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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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80 |
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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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83 |
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84 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use |
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85 the following command from the Galaxy root folder:: |
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86 |
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87 $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta |
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88 |
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89 Check this worked:: |
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90 |
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91 $ tar -tzf venn_list.tar.gz |
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92 tools/venn_list/README.rst |
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93 tools/venn_list/venn_list.py |
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94 tools/venn_list/venn_list.xml |
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95 tools/venn_list/tool_dependencies.xml |
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96 test-data/magic.pdf |
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97 test-data/venn_list.tabular |
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98 test-data/rhodopsin_proteins.fasta |
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99 |
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100 |
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101 Licence (MIT) |
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102 ============= |
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103 |
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104 Permission is hereby granted, free of charge, to any person obtaining a copy |
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105 of this software and associated documentation files (the "Software"), to deal |
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106 in the Software without restriction, including without limitation the rights |
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107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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108 copies of the Software, and to permit persons to whom the Software is |
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109 furnished to do so, subject to the following conditions: |
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110 |
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111 The above copyright notice and this permission notice shall be included in |
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112 all copies or substantial portions of the Software. |
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113 |
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114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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120 THE SOFTWARE. |