Mercurial > repos > peterjc > mummer
annotate tools/mummer/README.rst @ 6:d9f3d4779507 draft default tip
v0.0.7 stricter error checking; record gnuplot version
author | peterjc |
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date | Wed, 10 May 2017 12:14:49 -0400 |
parents | 683ea5ab0008 |
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rev | line source |
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1 Galaxy wrapper for drawing dotplots using MUMmer 3 |
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2 ================================================== |
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3 |
5 | 4 This wrapper is copyright 2014-2016 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 |
1
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8 This is a dotplot tool wrapping functionality from the MUMmer v3 suite. |
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9 |
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10 S. Kurtz et al. (2004). |
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11 Versatile and open software for comparing large genomes. |
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12 Genome Biology (2004), 5:R12. |
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13 http://dx.doi.org/10.1186/gb-2004-5-2-r12 |
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14 |
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15 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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16 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mummer |
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17 |
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18 Automated Installation |
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19 ====================== |
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20 |
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21 Automated installation from the Galaxy Tool Shed should be straightforward. |
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22 In addition to the wrapper itself, Galaxy should automatically download and |
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23 install the MUMmer files, gnuplot, and GhostScript which provides the |
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24 ``ps2pdf`` binary. |
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25 |
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26 |
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27 Manual Installation |
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28 =================== |
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29 |
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30 This expects MUMmer binaries (at least ``mummer``, ``nucmer``, ``promer``, and |
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31 ``mummerplot``) and the tools ``gnuplot`` and ``ps2pdf`` (from GhostScript) to |
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32 be on the system ``$PATH``. |
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33 |
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34 To install the wrapper copy or move the following files under the Galaxy tools |
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35 folder, e.g. in a ``tools/mummer`` folder: |
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36 |
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37 * ``mummer.xml`` (the Galaxy tool definition) |
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38 * ``mummer.py`` (the Python wrapper script) |
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39 * ``README.rst`` (this file) |
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40 |
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41 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the |
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42 tool. Just add the line:: |
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43 |
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44 <tool file="mummer/mummer.xml" /> |
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45 |
4 | 46 If you wish to run the unit tests, also move/copy the ``test-data/`` files |
47 under Galaxy's ``test-data/`` folder. Then:: | |
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48 |
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49 $ ./run_tests.sh -id mummerplot_wrapper |
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50 |
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51 That's it. |
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52 |
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53 |
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54 History |
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55 ======= |
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56 |
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57 ======= ====================================================================== |
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58 Version Changes |
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59 ------- ---------------------------------------------------------------------- |
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60 v0.0.1 - Initial public release. |
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61 v0.0.2 - Correct typo in Tool identifier. |
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62 - Include MUMmer citation in Galaxy XML markup. |
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63 v0.0.3 - Install ``ps2pdf`` using Tool Shed's GhostScript package. |
3
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64 v0.0.4 - Install ``gnuplot`` using Tool Shed's gnuplot package. |
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65 - Test case added. |
4 | 66 v0.0.5 - Reorder XML elements (internal change only). |
67 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
5 | 68 v0.0.6 - PEP8 style changes to Python script (internal change only). |
69 - Fixed display of input parameter help text. | |
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70 v0.0.7 - Use ``<command detect_errors="aggressive">`` (internal change only). |
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71 - Single quote command line arguments (internal change only). |
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72 - Wrapper script catches missing output explicitly. |
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73 - Capture gnuplot version as well. |
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74 ======= ====================================================================== |
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75 |
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76 |
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77 Developers |
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78 ========== |
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79 |
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80 Development is on GitHub at: |
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81 https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer |
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82 |
4 | 83 |
84 For pushing a release to the test or main "Galaxy Tool Shed", use the following | |
85 Planemo commands (which requires you have set your Tool Shed access details in | |
86 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
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87 |
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88 $ planemo shed_update -t testtoolshed --check_diff tools/mummer/ |
4 | 89 ... |
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90 |
4 | 91 or:: |
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92 |
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93 $ planemo shed_update -t toolshed --check_diff tools/mummer/ |
4 | 94 ... |
95 | |
96 To just build and check the tar ball, use:: | |
97 | |
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98 $ planemo shed_upload --tar_only tools/mummer/ |
4 | 99 ... |
100 $ tar -tzf shed_upload.tar.gz | |
101 test-data/magic.pdf | |
3
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102 test-data/magic.png |
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103 test-data/rhodopsin_nucs.fasta |
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104 test-data/three_human_mRNA.fasta |
4 | 105 tools/mummer/README.rst |
106 tools/mummer/mummer.py | |
107 tools/mummer/mummer.xml | |
108 tools/mummer/tool_dependencies.xml | |
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109 |
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110 |
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111 Licence (MIT) |
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112 ============= |
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113 |
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114 Permission is hereby granted, free of charge, to any person obtaining a copy |
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115 of this software and associated documentation files (the "Software"), to deal |
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116 in the Software without restriction, including without limitation the rights |
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117 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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118 copies of the Software, and to permit persons to whom the Software is |
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119 furnished to do so, subject to the following conditions: |
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120 |
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121 The above copyright notice and this permission notice shall be included in |
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122 all copies or substantial portions of the Software. |
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123 |
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124 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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125 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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126 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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127 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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128 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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129 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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130 THE SOFTWARE. |
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131 |
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132 NOTE: This is the licence for the Galaxy Wrapper only. |
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133 MUMmer is available and licenced separately. |