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Galaxy wrapper for OpenMS
=========================

OpenMS is an open-source software C++ library for LC/MS data management and analyses.
It offers an infrastructure for the rapid development of mass spectrometry related software.
OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.

More informations are available at:

 * https://github.com/OpenMS/OpenMS
 * http://open-ms.sourceforge.net


Installation
============

Galaxy should be able to automatically install the dependencies, i.e.
'package_openms_2_0' or 'package_qt_4_8' repository.

The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms.


Generating OpenMS wrappers
==========================

 * install OpenMS (you can do this automatically through the Tool Shed)
 * create a folder called CTD
 * inside of your new installed openms/bin folder, execute the following command:
    
    ```bash
    for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
    ```

 * clone or install CTDopts

    ```bash
    git clone https://github.com/genericworkflownodes/CTDopts
    ```

 * add CTDopts to your `$PYTHONPATH`

    ```bash
    export PYTHONPATH=/home/user/CTDopts/
    ```

 * clone or install GalaxyConfigGenerator

    ```bash
    git clone https://github.com/TorHou/GalaxyConfigGenerator.git
    ```
    
 * If you have CTDopts and GalaxyConfigGenerator installed you are ready to generate Galaxy Tools from CTD definitions

    ```bash
    python ./galaxyconfiggenerator/generator.py \ 
    -i /PATH/TO/YOUR/CTD*.ctd \
    -o ./wrappers -t tool.conf \
    -d OpenMS -g proteomics \
    -b version log debug test no_progress threads \
     in_type exe executable myrimatch_executable \
     omssa_executable pepnovo_executable \
     xtandem_executable \
    -l ListOfNeededTools.txt
    ```

The list of needed Tools is a whitelist of all Tools that you want to create. It's simply a list of all tools separated by line breaks.
An example file is located under https://gist.github.com/bgruening/421f97d36c27443e5f35


 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:

    ```
    sed -i '10 a\-exe fido' wrappers/FidoAdapter.xml
    sed -i '10 a\-executable msgfplus.jar' wrappers/MSGFPlusAdapter.xml
    sed -i '10 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
    sed -i '10 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
    sed -i '10 a\-pepnovo_executable pepnovo' wrappers/PepNovoAdapter.xml
    sed -i '10 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
    ```

Licence (MIT)
=============

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.