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1 # Tool - Generic Filter [Dockerfile]
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2
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3
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4 ## Metadata
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5
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6 - **@authors**: Nils Paulhe <nils.paulhe@inra.fr> (Only the docker part)
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7 - **@date creation**: `2017-09-04`
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8 - **@main usage**: create a Docker environment / container for "Tool - Generic Filter"
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9
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10 ## About
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11
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12 For all informations about the tool please refer to its [README file](README.md).
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13 For further information about Workflow4Metabolomics project and the people involved, please refer to [workflow4metabolomics.org](http://workflow4metabolomics.org/), [W4M github](https://github.com/workflow4metabolomics/) and [W4M Docker Hub](https://hub.docker.com/r/workflow4metabolomics/).
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14
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15 ## Configuration
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16
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17 ### Requirement:
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18 * Docker Engine, Docker skills
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19 * a Galaxy server docker compliant
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20
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21 ### Warning:
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22 * These scripts are provided WITHOUT ANY WARRANTY.
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23 * These scripts should be run by a system administrator (expert).
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24
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25 ## Services provided
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26
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27 Build a docker container for "Tool - Generic Filter" Galaxy Tool.
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28 Provide a XML Galaxy wrapper: generic_filter.docker.xml
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29
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30 ## Technical description
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31
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32 ### Create the docker container
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33
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34 ``` bash
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35 docker build -t workflow4metabolomics/tool-generic_filter:2017.06 .
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36 ```
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37
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38 ### Add the tool in Galaxy
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39
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40 Note: the files name and path are just examples. Adapt them to your own Galaxy configuration / practices.
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41
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42 If required, add in `config/job_conf.xml` file the minimal docker options:
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43
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44 ``` xml
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45 <destinations default="docker_local">
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46 <destination id="local" runner="local"/>
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47 <destination id="docker_local" runner="local">
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48 <param id="docker_enabled">true</param>
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49 <param id="docker_sudo">false</param>
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50 </destination>
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51 </destinations>
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52 ```
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53
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54 For more options please refer to the [official documentation](https://galaxyproject.org/admin/tools/docker/).
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55
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56 Copy or create a symbolic link of generic_filter.docker.xml file into your `tools/docker` directory (feel free to create or change the target directory).
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57 Then add this XML resource in your `config/tool_conf.xml` file. For example:
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58
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59 ``` xml
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60 <section id="docker_tools" name="Docker Tools">
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61 <tool file="docker/generic_filter.docker.xml"/>
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62 </section>
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63 ```
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64
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65 ### Modify this tool's XML config. file
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66
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67 replace these sections:
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68 ```xml
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69 <!-- requirements -->
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70 <requirements>
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71 <requirement type="package" version="1.1_4">r-batch</requirement>
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72 </requirements>
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73
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74 <!-- cmd -->
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75 <command>
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76 Rscript '$__tool_directory__/filter_wrap.R'
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77 dataMatrix_in "$dataMatrix_in"
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78 sampleMetadata_in "$sampleMetadata_in"
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79 <!-- ... -->
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80 ```
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81
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82 by these sections:
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83 ```xml
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84 <!-- requirements -->
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85 <requirements>
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86 <container type="docker">workflow4metabolomics/tool-generic_filter:2017.06</container>
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87 </requirements>
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88
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89 <!-- cmd -->
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90 /usr/bin/Rscript /scripts/filter_wrap.R
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91 dataMatrix_in "$dataMatrix_in"
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92 <!-- ... -->
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93 ```
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94
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95 ## License (Dockerfile only!)
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96
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97 The `Dockerfile` file is under the following license:
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98 ```
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99 Copyright (c) 2017 workflow4metabolomics.org / INRA
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100
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101 Permission is hereby granted, free of charge, to any person obtaining a copy
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102 of this software and associated documentation files (the "Software"), to deal
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103 in the Software without restriction, including without limitation the rights
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104 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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105 copies of the Software, and to permit persons to whom the Software is
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106 furnished to do so, subject to the following conditions:
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107
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108 The above copyright notice and this permission notice shall be included in all
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109 copies or substantial portions of the Software.
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110
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111 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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112 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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113 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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114 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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115 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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116 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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117 SOFTWARE.
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118 ```
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119
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120 - For the Galaxy Tool's license, please refer to its `README` file.
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121 - For the Galaxy Wrapper's license, please refer to its `XML` file.
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