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author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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1 ​ <img src="static/images/frogs_images/FROGS_logo.png" width="20%" style="display: block; margin: auto;"/> <img src="galaxy_project_logo_square.png" width="20%" style="display: block; margin: auto;"/>
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5 Visit our web site : http://frogs.toulouse.inra.fr/
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7 [![Release](https://img.shields.io/badge/release-3.1.0-blue.svg)![Date](https://img.shields.io/badge/date-February%202018-red.svg)](https://github.com/geraldinepascal/FROGS-wrappers/releases)[<img src="https://www.podcastscience.fm/wp-content/uploads/2017/12/deezer.png" width="5%" style="display: block; margin: auto;"/>](https://www.deezer.com/fr/playlist/5233843102?utm_source=deezer&utm_content=playlist-5233843102&utm_term=18632989_1545296531&utm_medium=web)
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11 # Description
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13 FROGS is a workflow designed to produce an OTU count matrix from high depth sequencing amplicon data.
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15 FROGS-wrapper allow to add FROGS on a Galaxy instance.
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17 # Table of content
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19 * [Installing FROGS\-wrappers](#installing-frogs-wrappers)
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20 * [Simplest way](#simplest-way)
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21 * [From sources](#from-sources)
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22 * [Prerequisites](#prerequisites)
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23 * [FROGS\-wrappers installation](#frogs-wrappers-installation)
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24 * [Use PEAR as reads merge software in preprocess](#use-pear-as-reads-merge-software-in-preprocess)
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25 * [Upload and configure the databanks](#upload-and-configure-the-databanks)
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26 * [Galaxy configuration](#galaxy-configuration)
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27 * [Setup Galaxy environment variables](#setup-galaxy-environment-variables)
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28 * [Install python packages inside virtual env](#install-python-packages-inside-virtual-env)
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29 * [Avoid FROGS HTML report sanitization](#avoid-FROGS-HTML-report-sanitization)
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30 * [Set memory and parallelisation settings](#set-memory-and-parallelisation-settings)
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31 * [License](#license)
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32 * [Copyright](#copyright)
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33 * [Citation](#citation)
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34 * [Contact](#contact)
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36 # Installing FROGS-wrappers
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38 ## Simplest way
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40 FROGS is available on the Toolshed : https://toolshed.g2.bx.psu.edu/repository?repository_id=525e78406276b403&changeset_revision=76c750c5f0d1
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42 It will install FROGS thanks to [conda](https://anaconda.org/bioconda/frogs), download all these XML tools and well configure them in your Galaxy.
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44 The 22 FROGS tools will be in random order in your tools panel. We propose to control that order by modifying the `integrated_tool_panel.xml `.
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46 We suppose that you installed FROGS in a spécific section named `FROGS` (update the FROGS version if necessary).
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48 ```
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49 <section id="FROGS" name="FROGS" version="">
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51 <label text="OTUs reconstruction" id="FROGS_OTU" />
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53 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_demultiplex/3.1" />
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54 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_preprocess/3.1" />
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55 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clustering/3.1" />
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56 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_remove_chimera/3.1" />
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57 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_filters/3.1" />
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58 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_itsx/3.1" />
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59 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_OTU/3.1" />
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60 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliation_postprocess/3.1" />
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61 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_normalisation/3.1" />
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62 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_Tree/3.1" />
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63 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_clusters_stat/3.1" />
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64 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_affiliations_stat/3.1" />
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65 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_stdBiom/3.1" />
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66 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_biom_to_tsv/3.1" />
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67 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGS_tsv_to_biom/3.1" />
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69 <label text="OTUs structure and composition analysis" id="FROGSSTAT_Phyloseq" />
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71 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Import_Data/3.1" />
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72 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Composition_Visualisation/3.1" />
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73 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Alpha_Diversity/3.1" />
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74 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Beta_Diversity/3.1" />
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75 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Sample_Clustering/3.1" />
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76 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Structure_Visualisation/3.1" />
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77 <tool id="toolshed.g2.bx.psu.edu/repos/frogs/frogs_3_1_0/FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance/3.1" />
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78 </section>
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79 ```
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80
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81
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82
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83 ## From sources
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84
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85 #### Prerequisites
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86
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87 You should start by installing [FROGS](https://github.com/geraldinepascal/FROGS) (remember, FROGS is now installable via [conda](https://anaconda.org/bioconda/frogs) )
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88
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89 #### FROGS-wrappers installation
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90
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91 1. <u>Download wrapper</u>
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92
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93 Download the last released versions of FROGS-wrappers: https://github.com/geraldinepascal/FROGS-wrappers/releases
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94
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95 Uncompress and unarchive the release in your ` <Galaxy_Dir>/tools` directory
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96
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97 (replace the) link to the new directory like this
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98
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99 ` ln -s <Galaxy_Dir>/tools/FROGS-wrappers-<Release_Number> <Galaxy_Dir>/tools/FROGS`
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100
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101 2. <u>Add tools in galaxy</u>
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102
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103 Add the tools in `<Galaxy_Dir>/config/tool_conf.xml`
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104
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105 ```
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106 <section id="FROGS_wrappers" name="FROGS">
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107 <label text="OTUs reconstruction" id="FROGS_OTU" />
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108 <tool file="FROGS/demultiplex.xml" />
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109 <tool file="FROGS/preprocess.xml" />
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110 <tool file="FROGS/clustering.xml" />
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111 <tool file="FROGS/remove_chimera.xml" />
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112 <tool file="FROGS/filters.xml" />
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113 <tool file="FROGS/itsx.xml" />
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114 <tool file="FROGS/affiliation_OTU.xml" />
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115 <tool file="FROGS/affiliation_postprocess.xml" />
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116 <tool file="FROGS/normalisation.xml" />
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117 <tool file="FROGS/tree.xml" />
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118 <tool file="FROGS/clusters_stat.xml" />
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119 <tool file="FROGS/affiliations_stat.xml" />
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120 <tool file="FROGS/biom_to_stdBiom.xml" />
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121 <tool file="FROGS/biom_to_tsv.xml" />
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122 <tool file="FROGS/tsv_to_biom.xml" />
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123 <label text="OTUs structure and composition analysis" id="FROGSSTAT_Phyloseq" />
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124 <tool file="FROGS/r_import_data.xml" />
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125 <tool file="FROGS/r_composition.xml" />
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126 <tool file="FROGS/r_alpha_diversity.xml" />
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127 <tool file="FROGS/r_beta_diversity.xml" />
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128 <tool file="FROGS/r_structure.xml" />
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129 <tool file="FROGS/r_clustering.xml" />
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130 <tool file="FROGS/r_manova.xml" />
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131 </section>
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132 ```
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133 NB: If you used previous version of FROGS, you must removed `app` direcotry name in the paths names.
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134
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135 3. <u>Add images</u>
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136
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137 Add the FROGS-wrappers images in `<Galaxy_Dir>/static/images` directory
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138
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139 `cp -r <Galaxy_Dir>/tools/FROGS/static/images/frogs_images/ <Galaxy_Dir>/static/images/.`
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140
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141
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142 # Use PEAR as reads merge software in preprocess
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143 [PEAR](https://cme.h-its.org/exelixis/web/software/pear/) is one of the most effective software for read pair merging, but as its licence is not free for private use, we can not distribute it in FROGS.
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144 If you work in an academic lab on a private Galaxy server, or if you have payed your licence you can use PEAR in FROGS preprocess.
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145 For that, you need to:
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146
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147 * have PEAR in your PATH or in the FROGS libexec directory
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148
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149 * add PEAR in the FROGS preprocess Galaxy wrapper (<FROGS_DIR>/tools/preprocess/preprocess.xml):
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150
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151 :warning: there is two places where the list merge_software is defined, add pear in both of them!
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152
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153 add pear value in the list of `merge_software`
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154 ```
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155 <conditional name="merge_software_type">
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156 <param name="merge_software" type="select" label="Merge software" help="Select the software to merge paired-end reads.">
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157 <option value="vsearch" selected="true">Vsearch</option>
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158 <option value="flash">Flash</option>
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159 <option value="pear">PEAR</option>
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160 </param>
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161 <when value="flash">
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162 <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" />
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163 </when>
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164 </conditional>
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165 ```
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166
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167 :warning: remember, there is two places where the list merge_software is defined, add pear in both of them!
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168
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169 # Upload and configure the databanks
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170
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171 Databanks are defined in `loc` files and `loc` files are defined in Galaxy datatable.
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172
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173 * Manual installation :
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174
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175 * datatables : `<Galaxy_Dir>/config/tool_data_table_conf.xml` , example : `<Galaxy_Dir>/tools/FROGS/tool_data_table_conf.xml.sample`
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176
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177 Add FROGS-wrappers datatables in the Galaxy datatables, but replace `{__HERE__}` by `tools/FROGS`.
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178
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179 * loc files example : `<Galaxy_Dir>/tools/FROGS/tool-data/`
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180
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181 Copy and rename them as indicated in the tool_data_table.
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182
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183 Then add entry as indicated in each loc files.
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184
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185 * Toolshed installation :
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186
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187 * datatables : `<Galaxy_Dir>/config/shed_tool_data_table_conf.xml` (nothing to modify, FROGS datatables should automatically be added)
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188 * loc files to filled in : `tool-data/toolshed.g2.bx.psu.edu/repos/frogs/frogs_<VERSION>/<RANDOM>/`
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189
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190
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191
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192 We provide some databanks for each of these 3 data tables, you simply need to download them and add them in the corresponding `loc` files.
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193
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194 - Assignation databank for affiliation_OTU tool
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195
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196 URL : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
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197
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198 loc file :`frogs_db.loc`
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199
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200 - Contaminant databank for filter tool
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201
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202 URL : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
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203
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204 loc file : `phiX_db.loc`
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205
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206 - Hyper variable in length amplicon databank for affiliation_postprocess tool
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207
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208 URL : http://genoweb.toulouse.inra.fr/frogs_databanks/HVL
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209
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210 loc file : `HVL.loc`
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211
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212
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213 # Galaxy configuration
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214
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215 ## setup Galaxy environment variables
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216
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217 FROGS python programs need to be available in the PATH, if installing from source or via conda, you need to add `<FROGS_PATH>/app` directory in the Galaxy PATH environment variable. (see [environment-setup-file parameter](https://docs.galaxyproject.org/en/latest/admin/config.html#environment-setup-file) )
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218
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219 ## Install python packages inside virtual env
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220
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221 Galaxy runs in a specific virtual env. To allow FROGS clusters stat to access to the python scipy library, you need to (re)install it inside the Galaxy virtual env
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222 ```
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223 cd <Galaxy_Dir>
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224 source .venv/bin/activate
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225 pip install scipy
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226 deactivate
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227 ```
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228
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229 ## Avoid FROGS HTML report sanitization
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230
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231 By default Galaxy sanitizes HTML outputs to prevent XSS attacks.
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232 FROGS outputs, for almost all tools, report in HTML format. To allow their visualization inside Galaxy, we need to avoid the Galaxy sanitization.
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233 You need to uncomment `sanitize_whitelist_file` line in `<Galaxy_Dir>/config/galaxy.ini`, create the corresponding `<Galaxy_Dir>/config/sanitize_whitelist.txt` file if not already done, and add the following lines in it.
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234 ```
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235 FROGSSTAT_Phyloseq_Alpha_Diversity
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236 FROGSSTAT_Phyloseq_Beta_Diversity
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237 FROGSSTAT_Phyloseq_Composition_Visualisation
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238 FROGSSTAT_Phyloseq_Import_Data
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239 FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance
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240 FROGSSTAT_Phyloseq_Sample_Clustering
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241 FROGSSTAT_Phyloseq_Structure_Visualisation
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242 FROGS_Tree
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243 FROGS_affiliation_OTU
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244 FROGS_affiliations_stat
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245 FROGS_clustering
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246 FROGS_clusters_stat
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247 FROGS_filters
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248 FROGS_itsx
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249 FROGS_normalisation
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250 FROGS_preprocess
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251 FROGS_remove_chimera
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252 ```
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253
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254 ## Set memory and parallelisation settings
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255
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256 If you have more than one CPU, it is recommended to increase the number of CPUs used by tools.
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257
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258 All CPUs must be on the same computer/node.
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259
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260
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261 * Specifications
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262
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263 | Tool | RAM per CPU | Minimal RAM | Configuration example |
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264 | :-------------------: | :---------: | :---------: | :-------------------: |
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265 | preprocess | 8Gb | - | 12 CPUs and 96 GB |
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266 | clustering | - | 10 Gb | 16 CPUs and 60 GB |
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267 | ITSx / remove_chimera | 3Gb | 5Gb | 12 CPUs and 36 GB |
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268 | affiliation_OTU | - | 20 Gb | 30 CPUs and 300 GB |
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269
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270 * Galaxy configuration
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271
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272 You need to add `destiantion` sections (one per tool) in the `<Galaxy-Dir>/config/job_conf.xml`
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273 Example for SGE scheduler:
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274
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275
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276 ```
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277 <destinations>
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278 ...
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279 <destination id="FROGS_preprocess_job" runner="drmaa">
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280 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
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281 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
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282 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
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283 <param id="nativeSpecification">-clear -q galaxyq -l mem=5G -l h_vmem=13G -pe parallel_smp 12</param>
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284 </destination>
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285 <destination id="FROGS_clustering_job" runner="drmaa">
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286 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
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287 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
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288 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
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289 <param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=10G -pe parallel_smp 16</param>
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290 </destination>
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291 <destination id="FROGS_remove_chimera_job" runner="drmaa">
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292 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
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293 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
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294 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
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295 <param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>
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296 </destination>
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297 <destination id="FROGS_itsx_job" runner="drmaa">
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298 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
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299 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
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300 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
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301 <param id="nativeSpecification">-clear -q galaxyq -l mem=3G -l h_vmem=4G -pe parallel_smp 12</param>
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302 </destination>
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303 <destination id="FROGS_affiliation_OTU_job" runner="drmaa">
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304 <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
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305 <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
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306 <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
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307 <param id="nativeSpecification">-clear -q galaxyq -l mem=7G -l h_vmem=10G -pe parallel_smp 30</param>
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308 </destination>
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309 </destinations>
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310 <tools>
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311 ...
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312 <tool id="FROGS_preprocess" destination="FROGS_preprocess_job"/>
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313 <tool id="FROGS_clustering" destination="FROGS_clustering_job"/>
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314 <tool id="FROGS_remove_chimera" destination="FROGS_remove_chimera_job"/>
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315 <tool id="FROGS_itsx" destination="FROGS_itsx_job"/>
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316 <tool id="FROGS_affiliation_OTU" destination="FROGS_affiliation_OTU_job"/>
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317 </tools>
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318 ```
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319
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320 # License
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321 GNU GPL v3
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322
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323 # Copyright
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324 2018 INRA
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325
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326 # Citation
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327 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
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328
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329 # Contact
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330 frogs@inra.fr
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331