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author melpetera
date Fri, 03 Jan 2020 04:09:28 -0500
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1 # Tool - Generic Filter [Dockerfile]
2
3
4 ## Metadata
5
6 - **@authors**: Nils Paulhe <nils.paulhe@inra.fr> (Only the docker part)
7 - **@date creation**: `2017-09-04`
8 - **@main usage**: create a Docker environment / container for "Tool - Generic Filter"
9
10 ## About
11
12 For all informations about the tool please refer to its [README file](README.md).
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/).
14
15 ## Configuration
16
17 ### Requirement:
18 * Docker Engine, Docker skills
19 * a Galaxy server docker compliant
20
21 ### Warning:
22 * These scripts are provided WITHOUT ANY WARRANTY.
23 * These scripts should be run by a system administrator (expert).
24
25 ## Services provided
26
27 Build a docker container for "Tool - Generic Filter" Galaxy Tool.
28 Provide a XML Galaxy wrapper: generic_filter.docker.xml
29
30 ## Technical description
31
32 ### Create the docker container
33
34 ``` bash
35 docker build -t workflow4metabolomics/tool-generic_filter:2017.06 .
36 ```
37
38 ### Add the tool in Galaxy
39
40 Note: the files name and path are just examples. Adapt them to your own Galaxy configuration / practices.
41
42 If required, add in `config/job_conf.xml` file the minimal docker options:
43
44 ``` xml
45 <destinations default="docker_local">
46 <destination id="local" runner="local"/>
47 <destination id="docker_local" runner="local">
48 <param id="docker_enabled">true</param>
49 <param id="docker_sudo">false</param>
50 </destination>
51 </destinations>
52 ```
53
54 For more options please refer to the [official documentation](https://galaxyproject.org/admin/tools/docker/).
55
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).
57 Then add this XML resource in your `config/tool_conf.xml` file. For example:
58
59 ``` xml
60 <section id="docker_tools" name="Docker Tools">
61 <tool file="docker/generic_filter.docker.xml"/>
62 </section>
63 ```
64
65 ### Modify this tool's XML config. file
66
67 replace these sections:
68 ```xml
69 <!-- requirements -->
70 <requirements>
71 <requirement type="package" version="1.1_4">r-batch</requirement>
72 </requirements>
73
74 <!-- cmd -->
75 <command>
76 Rscript '$__tool_directory__/filter_wrap.R'
77 dataMatrix_in "$dataMatrix_in"
78 sampleMetadata_in "$sampleMetadata_in"
79 <!-- ... -->
80 ```
81
82 by these sections:
83 ```xml
84 <!-- requirements -->
85 <requirements>
86 <container type="docker">workflow4metabolomics/tool-generic_filter:2017.06</container>
87 </requirements>
88
89 <!-- cmd -->
90 /usr/bin/Rscript /scripts/filter_wrap.R
91 dataMatrix_in "$dataMatrix_in"
92 <!-- ... -->
93 ```
94
95 ## License (Dockerfile only!)
96
97 The `Dockerfile` file is under the following license:
98 ```
99 Copyright (c) 2017 workflow4metabolomics.org / INRA
100
101 Permission is hereby granted, free of charge, to any person obtaining a copy
102 of this software and associated documentation files (the "Software"), to deal
103 in the Software without restriction, including without limitation the rights
104 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
105 copies of the Software, and to permit persons to whom the Software is
106 furnished to do so, subject to the following conditions:
107
108 The above copyright notice and this permission notice shall be included in all
109 copies or substantial portions of the Software.
110
111 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
112 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
113 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
114 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
115 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
116 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
117 SOFTWARE.
118 ```
119
120 - For the Galaxy Tool's license, please refer to its `README` file.
121 - For the Galaxy Wrapper's license, please refer to its `XML` file.