diff GalFilter/about_docker.md @ 3:cfd7c4aa5c26 draft default tip

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+# Tool - Generic Filter [Dockerfile]
+
+
+## Metadata
+
+- **@authors**: Nils Paulhe <[e-mail]> (Only the docker part)
+- **@date creation**: `2017-09-04`
+- **@main usage**: create a Docker environment / container for "Tool - Generic Filter"
+
+## About
+
+For all informations about the tool please refer to its [README file](README.md). 
+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/). 
+ 
+## Configuration
+
+### Requirement:
+ * Docker Engine, Docker skills
+ * a Galaxy server docker compliant
+
+### Warning:
+ * These scripts are provided WITHOUT ANY WARRANTY. 
+ * These scripts should be run by a system administrator (expert).
+
+## Services provided
+
+Build a docker container for "Tool - Generic Filter" Galaxy Tool.
+Provide a XML Galaxy wrapper: generic_filter.docker.xml
+ 
+## Technical description
+
+### Create the docker container
+
+``` bash
+docker build -t workflow4metabolomics/tool-generic_filter:2017.06 .
+```
+
+### Add the tool in Galaxy
+
+Note: the files name and path are just examples. Adapt them to your own Galaxy configuration / practices.
+
+If required, add in `config/job_conf.xml` file the minimal docker options:
+
+``` xml
+    <destinations default="docker_local">
+        <destination id="local" runner="local"/>
+        <destination id="docker_local" runner="local">
+          <param id="docker_enabled">true</param>
+          <param id="docker_sudo">false</param>
+       </destination>
+    </destinations>
+```
+
+For more options please refer to the [official documentation](https://galaxyproject.org/admin/tools/docker/).
+
+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). 
+Then add this XML resource in your `config/tool_conf.xml` file. For example:
+
+``` xml
+    <section id="docker_tools" name="Docker Tools">
+      <tool file="docker/generic_filter.docker.xml"/>
+    </section>
+```
+
+### Modify this tool's XML config. file
+
+replace these sections:
+```xml
+  <!-- requirements -->
+  <requirements>
+    <requirement type="package" version="1.1_4">r-batch</requirement>
+  </requirements>
+  
+  <!-- cmd -->
+  <command>
+    Rscript '$__tool_directory__/filter_wrap.R'
+      dataMatrix_in "$dataMatrix_in"
+      sampleMetadata_in "$sampleMetadata_in"
+      <!-- ... -->
+```
+
+by these sections:
+```xml
+  <!-- requirements -->
+  <requirements>
+    <container type="docker">workflow4metabolomics/tool-generic_filter:2017.06</container>
+  </requirements>
+  
+  <!-- cmd -->
+    /usr/bin/Rscript /scripts/filter_wrap.R
+      dataMatrix_in "$dataMatrix_in"
+      <!-- ... -->
+```
+
+## License (Dockerfile only!)
+
+The `Dockerfile` file is under the following license:
+```
+    Copyright (c) 2017 workflow4metabolomics.org / INRA
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in all
+    copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+    SOFTWARE.
+```
+
+- For the Galaxy Tool's license, please refer to its `README` file. 
+- For the Galaxy Wrapper's license, please refer to its `XML` file.