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annotate tools/clc_assembly_cell/README.rst @ 1:6c899e228df3 draft

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Uploaded v0.0.0a, include repository_dependencies.xml for samtools dependency
author peterjc
date Thu, 31 Oct 2013 07:59:32 -0400
parents 7b96d8a3262f
children 93ef6468b288
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1 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
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2 ==========================================================
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3
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4 This wrapper is copyright 2013 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 CLC Assembly Cell is the commercial command line assembly suite from CLCbio.
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9 It uses SIMD instructions to parallelize and accelerate their assembly
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10 algorithms, and is also very memory efficient making it an appealing choice
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11 for complex genomes where the RAM requirements exclude other popular tools.
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12
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13 For more information:
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14 http://www.clcbio.com/products/clc-assembly-cell/
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15
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16 You can download the CLC Assembly Cell User Manual here, currently v4.2
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17 http://www.clcbio.com/files/usermanuals/CLC_Assembly_Cell_User_Manual.pdf
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18
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19 There is also an online manual here:
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20 http://clcsupport.com/clcassemblycell/current/index.php?manual=Introduction.html
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21
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22 There is currently a free trial download here:
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23 http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95
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24
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25 This wrapper is available from the Galaxy Tool Shed at:
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26 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
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27
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28 This Galaxy wrapper was written and tested using CLC Assembly Cell
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29 version 4.10.86742
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32 Automated Installation
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33 ======================
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34
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35 This should be straightforward, Galaxy should automatically download and
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36 install the wrapper from the Galaxy Tool Shed. However, you will need to
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37 manually install the CLC Assembly Cell software, and setup the environment
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38 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
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39 (and in particular, the ``clc_assembler`` binary). For example:
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40
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41 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
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42
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43
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44 Manual Installation
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45 ===================
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46
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47 First install the CLC Assembly Cell sortware as described above.
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48
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49 To install the wrapper copy or move the following files under the Galaxy tools
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50 folder, e.g. in a tools/clcbio folder:
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51
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52 * clc_assembler.xml (Galaxy tool definition)
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53 * clc_mapper.xml (Galaxy tool definition)
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54 * README.rst (this file)
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55
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56 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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57 tools. Just all these line, for example next to other assembly tools::
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58
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59 <tool file="clc_assembly_cell/clc_assembler.xml" />
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60 <tool file="clc_assembly_cell/clc_mapper.xml" />
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61
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62 If you wish to run the unit tests, also add this to tools_conf.xml.sample
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63 and move/copy the test-data files under Galaxy's test-data folder. Then::
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64
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65 $ ./run_functional_tests.sh -id clc_assembler
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66
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67 That's it.
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68
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69
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70 History
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71 =======
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72
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73 ======= ======================================================================
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74 Version Changes
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75 ------- ----------------------------------------------------------------------
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76 v0.0.1 - Initial public release
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77 ======= ======================================================================
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78
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79
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80 Developers
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81 ==========
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82
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83 Development is on this itHub repository:
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84 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
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85
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86 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
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87 the following command from the Galaxy root folder::
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88
1
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89 $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/repository_dependencies.xml
0
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90
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91 Check this worked::
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92
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93 $ tar -tzf clcbio.tar.gz
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94 tools/clc_assembly_cell/README.rst
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95 tools/clc_assembly_cell/clc_assembler.xml
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96 tools/clc_assembly_cell/clc_mapper.xml
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97 tools/clc_assembly_cell/repository_dependencies.xml
0
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98
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99
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100 Licence (MIT)
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101 =============
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102
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103 Permission is hereby granted, free of charge, to any person obtaining a copy
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104 of this software and associated documentation files (the "Software"), to deal
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105 in the Software without restriction, including without limitation the rights
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106 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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107 copies of the Software, and to permit persons to whom the Software is
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108 furnished to do so, subject to the following conditions:
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109
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110 The above copyright notice and this permission notice shall be included in
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111 all copies or substantial portions of the Software.
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112
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113 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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114 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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115 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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116 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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117 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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118 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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119 THE SOFTWARE.
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120
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121 NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are
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122 commercial, and are available and licenced separately.