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1 Galaxy wrapper for OpenMS
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2 =========================
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3
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4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
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5 It offers an infrastructure for the rapid development of mass spectrometry related software.
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6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
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7
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8 More informations are available at:
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9
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10 * https://github.com/OpenMS/OpenMS
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11 * http://open-ms.sourceforge.net
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12
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13
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14 Installation
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15 ============
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16
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17 Galaxy should be able to automatically install the dependencies, i.e.
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18 'package_openms_2_0' or 'package_qt_4_8' repository.
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19
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20 The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms.
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21
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22
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23 Generating OpenMS wrappers
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24 ==========================
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25
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26 * install OpenMS (you can do this automatically through the Tool Shed)
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27 * create a folder called CTD
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28 * inside of your new installed openms/bin folder, execute the following command:
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29
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30 ```bash
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31 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
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32 ```
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33
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34 * clone or install CTDopts
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35
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36 ```bash
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37 git clone https://github.com/genericworkflownodes/CTDopts
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38 ```
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39
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40 * add CTDopts to your `$PYTHONPATH`
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41
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42 ```bash
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43 export PYTHONPATH=/home/user/CTDopts/
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44 ```
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45
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46 * clone or install GalaxyConfigGenerator
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47
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48 ```bash
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49 git clone https://github.com/TorHou/GalaxyConfigGenerator.git
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50 ```
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51
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52 * If you have CTDopts and GalaxyConfigGenerator installed you are ready to generate Galaxy Tools from CTD definitions
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53
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54 ```bash
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55 python ./galaxyconfiggenerator/generator.py \
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56 -i /PATH/TO/YOUR/CTD*.ctd \
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57 -o ./wrappers -t tool.conf \
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58 -d OpenMS -g proteomics \
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59 -b version log debug test no_progress threads \
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60 in_type exe executable myrimatch_executable \
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61 omssa_executable pepnovo_executable \
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62 xtandem_executable \
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63 -l ListOfNeededTools.txt
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64 ```
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65
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66 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.
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67 An example file is located under https://gist.github.com/bgruening/421f97d36c27443e5f35
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68
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69
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70 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
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71
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72 ```
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73 sed -i '10 a\-exe fido' wrappers/FidoAdapter.xml
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74 sed -i '10 a\-executable msgfplus.jar' wrappers/MSGFPlusAdapter.xml
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75 sed -i '10 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
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76 sed -i '10 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
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77 sed -i '10 a\-pepnovo_executable pepnovo' wrappers/PepNovoAdapter.xml
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78 sed -i '10 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
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79 ```
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80
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81 Licence (MIT)
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82 =============
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83
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84 Permission is hereby granted, free of charge, to any person obtaining a copy
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85 of this software and associated documentation files (the "Software"), to deal
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86 in the Software without restriction, including without limitation the rights
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87 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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88 copies of the Software, and to permit persons to whom the Software is
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89 furnished to do so, subject to the following conditions:
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90
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91 The above copyright notice and this permission notice shall be included in
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92 all copies or substantial portions of the Software.
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93
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94 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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95 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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96 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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97 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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98 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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99 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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100 THE SOFTWARE.
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101
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