Mercurial > repos > galaxyp > openms_mapstatistics
annotate readme.md @ 0:e4c1d9a768db draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:37:14 -0500 |
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children | 67c01c07bbc1 |
rev | line source |
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e4c1d9a768db
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 Galaxy wrapper for OpenMS |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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2 ========================= |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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4 OpenMS is an open-source software C++ library for LC/MS data management and analyses. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 It offers an infrastructure for the rapid development of mass spectrometry related software. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 More informations are available at: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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10 * https://github.com/OpenMS/OpenMS |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 * http://open-ms.sourceforge.net |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 Generating OpenMS wrappers |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 ========================== |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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16 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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17 * install OpenMS (you can do this automatically through the Tool Shed) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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18 * create a folder called CTD |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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19 * inside of your new installed openms/bin folder, execute the following command: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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20 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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21 ```bash |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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23 ``` |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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24 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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25 * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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26 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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27 * clone or install CTDopts |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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28 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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29 ```bash |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 git clone https://github.com/genericworkflownodes/CTDopts |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 ``` |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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32 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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33 * add CTDopts to your `$PYTHONPATH` |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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34 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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35 ```bash |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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36 export PYTHONPATH=/home/user/CTDopts/ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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37 ``` |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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38 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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39 * clone or install CTD2Galaxy |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 ```bash |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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42 git clone https://github.com/blankclemens/CTD2Galaxy.git |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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43 ``` |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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44 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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45 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. |
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46 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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47 ```bash |
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48 python generator.py \ |
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49 -i /PATH/TO/YOUR/CTD/*.ctd \ |
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50 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ |
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51 -d datatypes_conf.xml -g openms \ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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52 -b version log debug test no_progress threads \ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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53 in_type executable myrimatch_executable \ |
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54 fido_executable fidocp_executable \ |
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55 omssa_executable pepnovo_executable \ |
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56 xtandem_executable param_model_directory \ |
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57 java_executable java_memory java_permgen \ |
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58 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ |
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59 -s PATH/TO/SKIP_TOOLS_FILES.txt |
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60 ``` |
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61 |
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62 |
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63 * 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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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64 |
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65 ``` |
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66 sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml |
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67 sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml |
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68 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml |
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69 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml |
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70 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml |
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71 ``` |
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72 |
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73 * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): |
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74 |
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75 ``` |
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76 <command><![CDATA[ |
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77 |
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78 ## check input file type |
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79 #set $in_type = $param_in.ext |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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80 |
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81 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files |
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82 ln -s '$param_in' 'param_in.${in_type}' && |
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83 ln -s '$param_database' param_database.fasta && |
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84 ## find location of the MSGFPlus.jar file of the msgf_plus conda package |
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85 MSGF_JAR=\$(msgf_plus -get_jar_path) && |
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86 |
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87 MSGFPlusAdapter |
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88 -executable \$MSGF_JAR |
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89 #if $param_in: |
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90 -in 'param_in.${in_type}' |
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91 #end if |
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92 #if $param_out: |
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93 -out $param_out |
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94 #end if |
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95 #if $param_mzid_out: |
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96 -mzid_out $param_mzid_out |
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97 #end if |
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98 #if $param_database: |
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99 -database param_database.fasta |
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100 #end if |
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101 |
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102 [...] |
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103 ]]> |
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104 ``` |
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105 * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line |
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106 |
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107 -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit |
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108 |
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109 and change it to |
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110 |
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111 -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" |
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112 |
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113 * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: |
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114 |
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115 <data name="param_out" metadata_source="param_in" auto_format="true"/> |
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116 |
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117 * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. |
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118 |
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119 ``` |
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120 <tests> |
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121 <test> |
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122 <param name="param_in" value="DecoyDatabase_input.fasta"/> |
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123 <output name="param_out" file="DecoyDatabase_output.fasta"/> |
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124 </test> |
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125 </tests> |
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126 ``` |
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127 |
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128 |
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129 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`: |
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130 * SeedListGenerator |
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131 * SpecLibSearcher |
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132 * MapAlignerIdentification |
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133 * MapAlignerPoseClustering |
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134 * MapAlignerSpectrum |
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135 * MapAlignerRTTransformer |
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136 |
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137 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: |
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138 * OMSSAAdapter |
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139 * MyrimatchAdapter |
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140 |
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141 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: |
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142 * PepNovoAdapter |
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143 |
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144 |
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145 Licence (MIT) |
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146 ============= |
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147 |
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148 Permission is hereby granted, free of charge, to any person obtaining a copy |
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149 of this software and associated documentation files (the "Software"), to deal |
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150 in the Software without restriction, including without limitation the rights |
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151 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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152 copies of the Software, and to permit persons to whom the Software is |
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153 furnished to do so, subject to the following conditions: |
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154 |
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155 The above copyright notice and this permission notice shall be included in |
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156 all copies or substantial portions of the Software. |
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157 |
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158 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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159 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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160 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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161 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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162 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
e4c1d9a768db
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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163 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
e4c1d9a768db
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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164 THE SOFTWARE. |
e4c1d9a768db
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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165 |