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Uploaded version 1.0.2.0.
author pjbriggs
date Thu, 01 Sep 2016 04:23:27 -0400
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1 RnaChipIntegrator: integrated analysis of gene expression and ChIP data
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2 =======================================================================
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4 Galaxy tool wrappers for running the RnaChipIntegrator program
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5 (http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated
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6 analyses of gene expression and ChIP data.
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8 There are two tools available that are built around RnaChipIntegrator:
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10 - General RnaChipIntegrator tool that allows any peaks to be analysed against
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11 any gene list
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12 - A "cannonical gene" variant which allows ChIP peaks to be analysed against a
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13 list of cannonical genes for different genomes
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15 Automated installation
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16 ======================
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18 Installation via the Galaxy Tool Shed will take of installing the tool wrapper
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19 and the RnaChipIntegrator programs, installing the .loc files, and setting the
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20 appropriate environment variables.
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22 Manual Installation
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23 ===================
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25 There are three files to install:
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27 - ``rnachipintegrator_wrapper.xml`` (the Galaxy tool definition for general usage)
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28 - ``rnachipintegrator_canonical_genes.xml`` (tool definition for the "canonical
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29 gene" variant)
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30 - ``rnachipintegrator_wrapper.sh`` (the shell script wrapper)
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32 The suggested location is in a ``tools/rnachipintegrator/`` folder. You will then
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33 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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34 by adding the lines:
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36 <tool file="rnachipintegrator/rnachipintegrator_wrapper.xml" />
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37 <tool file="rnachipintegrator/rnachipintegrator_canonical_genes.xml" />
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39 You will also need to install the RnaChipIntegrator program:
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41 - http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
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43 In addition for the cannonical gene and histone modification variants, it's
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44 necessary to copy the .loc.sample files to .loc Galaxy's ``tool-data`` folder:
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46 - **Cannonical genes**: its necessary to manually acquire cannonical gene
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47 list files from UCSC and then add appropriate references in the
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48 ``rnachipintegrator_canonical_genes.loc`` file.
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50 If you want to run the functional tests, copy the sample test files under
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51 ``test-data`` to Galaxy's ``test-data/`` directory. Then:
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53 ./run_tests.sh -id fls_rnachipintegrator_wrapper
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56 How to get canonical gene data
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57 ==============================
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59 Getting canonical gene info from UCSC is covered in the screencast at
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60 http://blog.openhelix.eu/?p=6097
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62 In summary:
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64 - **UCSC genome browser:** if multiple versions of each gene are visible (e.g.
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65 if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000)
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66 then:
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68 - Scroll down to the Gene & Gene Prediction section
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69 - Click on the UCSC genes link
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70 - Uncheck the tickbox next to splice variants and resubmit to view without
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71 duplicates.
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73 - **UCSC table browser:** to obtain the canonical set of genes from the table
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74 browser:
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76 - Select knownCanonical from the table menu
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77 - Select selected fields from primary & related tables from the output format menu
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78 - Click on Get output
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79 - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the
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80 'knownCanonical' table plus 'geneSymbol' from the kgXref table.)
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81 - Click on Get output to get the data for download
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83 (Hint: to also get strand direction information i.e. +/-, also allow selection
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84 from the refGene table, and select the strand field.)
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85
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86
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87 Note on Excel output files and Galaxy
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88 =====================================
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89
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90 RnaChipIntegrator produces an Excel spreadsheet as one of its outputs,
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91 however Galaxy is not currently set up by default to handle these.
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92
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93 To enable Excel (XLS) output file handling in Galaxy, edit the
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94 ``datatypes_conf.xml`` file and add:
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95
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96 <datatype extension="xlsx" type="galaxy.datatypes.binary:Binary" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/>
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97
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98 Restarting Galaxy should mean that the browser correctly handles Excel outputs
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99 from RnaChipIntegrator.
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100
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101 History
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102 =======
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103
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104 ========== ======================================================================
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105 Version Changes
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106 ---------- ----------------------------------------------------------------------
2
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107 1.0.2.0 - Update to ``RnaChipIntegrator`` version 1.0.2 (fixes bug with
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108 zero or blank cutoff)
0
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109 1.0.0.0 - Update to use latest ``RnaChipIntegrator`` version 1.0.0.
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110 0.5.0-0 - Significant update to bring tools in line with
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111 ``RnaChipIntegrator`` version 0.5.0, including removing the
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112 distinction between 'regions' and 'summits' for input peaks,
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113 and otherwise attempting to simplify the tools for users.
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114 0.4.4-0 - Initial version pushed to toolshed
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115 ========== ======================================================================
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116
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117
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118 Developers
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119 ==========
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120
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121 This tool is developed on the following GitHub repository:
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122 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator
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123
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124 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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125 the ``package_rnachipintegrator_wrapper.sh`` script.
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126
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127
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128 Licence (MIT)
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129 =============
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130
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131 Permission is hereby granted, free of charge, to any person obtaining a copy
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132 of this software and associated documentation files (the "Software"), to deal
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133 in the Software without restriction, including without limitation the rights
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134 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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135 copies of the Software, and to permit persons to whom the Software is
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136 furnished to do so, subject to the following conditions:
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137
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138 The above copyright notice and this permission notice shall be included in
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139 all copies or substantial portions of the Software.
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140
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141 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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142 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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143 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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144 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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145 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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146 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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147 THE SOFTWARE.