Mercurial > repos > peterjc > venn_list
annotate tools/venn_list/README.rst @ 6:ea68a1a4c1d9 draft
v0.0.10 explicit galaxy_sequence_utils dependency etc
author | peterjc |
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date | Thu, 02 Feb 2017 11:17:31 -0500 |
parents | 26e35d5133a1 |
children | ee50d9ef9d69 |
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 |
6
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4 This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute |
4
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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 |
5 | 21 and the Python dependencies Biopython and rpy, and the R/Bioconductor package |
22 limma. | |
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23 |
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24 |
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25 Manual Installation |
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26 =================== |
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27 |
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28 There are just two files to install: |
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29 |
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30 * ``venn_list.py`` (the Python script) |
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31 * ``venn_list.xml`` (the Galaxy tool definition) |
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32 |
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33 The suggested location is in the Galaxy folder ``tools/plotting`` next to other |
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34 graph drawing tools, or a dedicated ``tools/venn_list`` directory. |
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35 |
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36 You will also need to install Biopython 1.54 or later, and the R/Bioconductor |
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37 package limma. You should already have rpy installed for other Galaxy tools. |
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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. The suggested location is in the "Graph/Display Data" section. Simply add |
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41 the line:: |
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42 |
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43 <tool file="venn_list/venn_list.xml" /> |
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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 venn_list |
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49 |
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50 |
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51 History |
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52 ======= |
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53 |
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54 ======= ====================================================================== |
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55 Version Changes |
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56 ------- ---------------------------------------------------------------------- |
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57 v0.0.3 - Initial public release. |
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58 v0.0.4 - Ignore blank lines when loading IDs from tabular files |
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59 v0.0.5 - Explicit Galaxy error handling of return codes |
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60 v0.0.6 - Added unit tests. |
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61 - Use reStructuredText for this README file. |
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62 - Adopt standard MIT licence. |
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63 - Updated citation information (Cock et al. 2013). |
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64 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy |
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65 v0.0.7 - Renamed folder and README file. |
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66 - Tool definition now embeds citation information. |
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67 v0.0.8 - Reorder XML elements (internal change only). |
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68 - Fixed and improved error handling when rpy is not available. |
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69 - Test output relaxed to cope with more variation in PDF output. |
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70 - Declare Biopython dependency via the Tool Shed. |
5 | 71 v0.0.9 - Test with three-way Venn diagram. |
72 - Includes testing of failure mode. | |
73 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
74 - Tool Shed dependency for rpy and limma (thanks to Björn Grüning). | |
6
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75 v0.0.10 - Updated to point at Biopython 1.67 (latest version in Tool Shed). |
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76 - Explicit dependency on ``galaxy_sequence_utils``. |
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77 - Python style updates (internal change only). |
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78 ======= ====================================================================== |
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79 |
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80 |
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81 Developers |
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82 ========== |
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83 |
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84 This script and related tools were initially developed on the following hg branch: |
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85 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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86 |
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87 Development has now moved to a dedicated GitHub repository: |
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88 https://github.com/peterjc/pico_galaxy |
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89 |
5 | 90 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
91 Planemo commands (which requires you have set your Tool Shed access details in | |
92 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
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93 |
5 | 94 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ |
95 ... | |
96 | |
97 or:: | |
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98 |
5 | 99 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/ |
100 ... | |
101 | |
102 To just build and check the tar ball, use:: | |
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103 |
5 | 104 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/venn_list/ |
105 ... | |
106 $ tar -tzf shed_upload.tar.gz | |
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107 tools/venn_list/README.rst |
5 | 108 tools/venn_list/tool_dependencies.xml |
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109 tools/venn_list/venn_list.py |
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110 tools/venn_list/venn_list.xml |
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111 test-data/magic.pdf |
5 | 112 test-data/rhodopsin_proteins.fasta |
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113 test-data/venn_list.tabular |
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114 |
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115 |
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116 Licence (MIT) |
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117 ============= |
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118 |
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119 Permission is hereby granted, free of charge, to any person obtaining a copy |
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120 of this software and associated documentation files (the "Software"), to deal |
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121 in the Software without restriction, including without limitation the rights |
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122 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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123 copies of the Software, and to permit persons to whom the Software is |
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124 furnished to do so, subject to the following conditions: |
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125 |
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126 The above copyright notice and this permission notice shall be included in |
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127 all copies or substantial portions of the Software. |
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128 |
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129 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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130 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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131 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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132 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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133 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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134 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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135 THE SOFTWARE. |