Mercurial > repos > peterjc > mira4_9_mirabait

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
author peterjc
date Wed, 07 Oct 2015 10:31:49 -0400
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c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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1 Galaxy wrapper for the MIRA assembly program (v4.9) mirabait
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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 (MIT licence).
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8 This is a Galaxy wrapper for ``mirabait`` from the MIRA 4.9 assembly suite.
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10 It is available from the Galaxy Tool Shed at:
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11 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
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13 Development/test previews are available from the Galaxy Test Tool Shed at:
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14 http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_9_mirabait
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16 It is part of a suite for all the MIRA 4.9 tools:
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17 TODO...
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19 A separate wrapper for MIRA v4.0 is available from the Galaxy Tool Shed at:
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20 http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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23 Automated Installation
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24 ======================
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26 This should be straightforward. Via the Tool Shed, Galaxy should automatically
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27 install the precompiled binaries for MIRA v4.9.5, and offer to run any tests.
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30 Manual Installation
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31 ===================
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33 There are various Python and XML files to install into Galaxy:
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35 * ``mira4_9_mirabait.xml`` (the Galaxy tool definition for mirabait)
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36 * ``mira_check_version.py`` (Python helper script)
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37
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38 The suggested location is a new ``tools/mira4_9`` folder. You will
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39 also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
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40 tool::
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42 <tool file="mira4_9/mirabait/mira4_9_mirabait.xml" />
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43 ...
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45 You will also need to install MIRA 4.9, we used version 4.9.5, and define the
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46 environment variable ``$MIRA4_9`` pointing at the folder containing the
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47 binaries. See:
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49 * http://chevreux.org/projects_mira.html
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50 * http://sourceforge.net/projects/mira-assembler/
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52 You may wish to use different cluster setups for the de novo and mapping
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53 tools, see above.
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55 You will also need to install samtools (for generating a BAM file from MIRA's
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56 SAM output).
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58 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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59 under Galaxy's ``test-data/`` folder. Then::
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61 $ ./run_tests.sh -id mira4_9_mirabait
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62 ...
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65 History
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66 =======
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68 ======= ======================================================================
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69 Version Changes
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70 ------- ----------------------------------------------------------------------
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71 v0.0.1 - Initial version for MIRA 4.9.5, based on wrapper for v4.0.2
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72 ======= ======================================================================
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75 Developers
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76 ==========
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78 Development is on a dedicated GitHub repository:
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79 https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9
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81 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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82 Planemo commands (which requires you have set your Tool Shed access details in
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83 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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85 $ planemo shed_update -t testtoolshed --check_diff tools/mira4_9/
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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86 ...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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87
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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88 or::
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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89
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
peterjc
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90 $ planemo shed_update -t toolshed --check_diff tools/mira4_9/
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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91 ...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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92
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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93 To just build and check the tar ball, use::
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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94
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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95 $ planemo shed_upload --tar_only mira4_9/
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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96 ...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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97 $ tar -tzf shed_upload.tar.gz
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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98 ...
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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99
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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100
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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101 Licence (MIT)
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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102 =============
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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103
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104 Permission is hereby granted, free of charge, to any person obtaining a copy
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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105 of this software and associated documentation files (the "Software"), to deal
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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106 in the Software without restriction, including without limitation the rights
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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108 copies of the Software, and to permit persons to whom the Software is
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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109 furnished to do so, subject to the following conditions:
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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110
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111 The above copyright notice and this permission notice shall be included in
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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112 all copies or substantial portions of the Software.
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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113
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114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
c9269b5803d8 planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_9 commit 9a6640a7b7f516d028a9852f7bbf39083e50188f
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120 THE SOFTWARE.