annotate tools/clc_assembly_cell/README.rst @ 5:31a9169b6222 draft default tip

"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:32:53 +0000
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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 2013-2017 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 v4.1.0,
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29 specifically ``clc_assember`` and ``clc_mapper`` binaries for 64 bit Linux
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30 which report version 4.10.86742 at the command line.
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33 Automated Installation
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34 ======================
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35
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36 This should be straightforward, Galaxy should automatically download and
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37 install the wrapper from the Galaxy Tool Shed. However, you will need to
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38 manually install the CLC Assembly Cell software, and setup the environment
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39 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
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40 (in particular, binaries ``clc_assembler``, ``clc_mapper`` and
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41 ``clc_cas_to_sam``). For example::
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42
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43 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
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45 If your CLC Bio licence is restricted to specific machines on your cluster,
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46 use Galaxy's job configuration settings to ensure CLC jobs are only sent
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47 to those licenced computers. For SGE, we use the ``-l hostname="..."``
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48 option to do this. Alternatively your cluster administrator might setup
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49 a dedicated job queue.
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51
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52 Manual Installation
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53 ===================
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54
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55 First install the CLC Assembly Cell sortware as described above.
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56
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57 To install the wrapper copy or move the following files under the Galaxy tools
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58 folder, e.g. in a ``tools/clcbio/`` folder:
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59
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60 * ``clc_assembler.xml`` (Galaxy tool definition)
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61 * ``clc_mapper.xml`` (Galaxy tool definition)
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62 * ``README.rst`` (this file)
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63
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64 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
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65 the tools. Just all these line, for example next to other assembly tools::
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66
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67 <tool file="clc_assembly_cell/clc_assembler.xml" />
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68 <tool file="clc_assembly_cell/clc_mapper.xml" />
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69
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70 If you wish to run the unit tests, also move/copy the ``test-data/`` files
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71 under Galaxy's ``test-data/`` folder. Then run::
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72
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73 $ ./run_tests.sh -id clc_assembler
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74 $ ./run_tests.sh -id clc_mapper
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75
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76 That's it.
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78
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79 History
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80 =======
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81
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82 ======= ======================================================================
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83 Version Changes
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84 ------- ----------------------------------------------------------------------
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85 v0.0.1 - Initial public release.
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86 v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable.
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87 - Enable and fixed the tests.
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88 v0.0.3 - Reorder XML elements (internal change only).
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89 - Added citation tags.
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90 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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139b6f0a0bb5 v0.0.4 fix recording of clc version
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91 v0.0.4 - Bug fix for ``<version_command>`` to capture tool version.
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92 v0.0.5 - Support the ``-u`` or ``--discardunmapped`` option to discard
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93 unmapped reads in the CLC Mapper wrapper.
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94 - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when
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95 calling ``clc_cas_to_sam`` in the CLC MApper wrapper.
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96 v0.0.6 - Update tool XML for optional vs required parameters.
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97 - Update URLs in documentation.
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98 v0.0.7 - Use ``<command detect_errors="aggressive">`` (internal change only).
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99 - Single quote command line arguments (internal change only).
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100 ======= ======================================================================
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101
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102
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103 Developers
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104 ==========
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105
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106 Development is on this itHub repository:
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107 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
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108
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109 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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110 Planemo commands (which requires you have set your Tool Shed access details in
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111 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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112
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113 $ planemo shed_update -t testtoolshed --check_diff tools/clc_assembly_cell/
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114 ...
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115
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116 or::
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117
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118 $ planemo shed_update -t toolshed --check_diff tools/clc_assembly_cell/
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119 ...
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120
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121 To just build and check the tar ball, use::
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122
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123 $ planemo shed_upload --tar_only tools/clc_assembly_cell/
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124 ...
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125 $ tar -tzf shed_upload.tar.gz
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126 test-data/NC_010642.fna
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127 tools/clc_assembly_cell/README.rst
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128 tools/clc_assembly_cell/clc_assembler.xml
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129 tools/clc_assembly_cell/clc_mapper.xml
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130 tools/clc_assembly_cell/tool_dependencies.xml
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131
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132
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133 Licence (MIT)
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134 =============
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135
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136 Permission is hereby granted, free of charge, to any person obtaining a copy
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137 of this software and associated documentation files (the "Software"), to deal
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138 in the Software without restriction, including without limitation the rights
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139 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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140 copies of the Software, and to permit persons to whom the Software is
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141 furnished to do so, subject to the following conditions:
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142
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143 The above copyright notice and this permission notice shall be included in
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144 all copies or substantial portions of the Software.
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145
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146 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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147 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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148 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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149 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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150 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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151 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
0996169ac2e8 Uploaded v0.0.2, previously only on the TestToolShed
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152 THE SOFTWARE.
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153
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154 NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are
0996169ac2e8 Uploaded v0.0.2, previously only on the TestToolShed
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155 commercial, and are available and licenced separately.