Mercurial > repos > galaxyp > openms_qcextractor
annotate readme.md @ 2:550c87b6eea5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author | galaxyp |
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date | Wed, 18 Oct 2017 15:37:06 -0400 |
parents | 6c4b0427c053 |
children | e2eb1f850949 |
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6a16b2a96a5e
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 |
6a16b2a96a5e
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 |
6a16b2a96a5e
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. |
6a16b2a96a5e
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 |
6a16b2a96a5e
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 |
6a16b2a96a5e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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12 |
6a16b2a96a5e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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13 |
6a16b2a96a5e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 Generating OpenMS wrappers |
6a16b2a96a5e
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 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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17 * install OpenMS (you can do this automatically through Conda) |
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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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6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: |
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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; |
6a16b2a96a5e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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23 ``` |
6a16b2a96a5e
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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6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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26 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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27 ```bash |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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28 ls >> tools.txt |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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29 ``` |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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30 |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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31 * search for the `bin` folder of your conda environment containing OpenMS and do: |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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32 |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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33 ```bash |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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34 while read p; do |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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36 done <tools.txt |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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37 ``` |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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38 |
6c4b0427c053
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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39 * You should have all CTD files now. `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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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 * 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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42 |
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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 ```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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44 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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45 ``` |
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46 |
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47 * add CTDopts to your `$PYTHONPATH` |
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48 |
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49 ```bash |
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50 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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51 ``` |
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52 |
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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 * 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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54 |
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55 ```bash |
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56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git |
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57 ``` |
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58 |
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59 * 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. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. |
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60 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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61 ```bash |
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62 python generator.py \ |
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63 -i /PATH/TO/YOUR/CTD/*.ctd \ |
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64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ |
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65 -d datatypes_conf.xml -g openms \ |
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66 -b version log debug test no_progress threads \ |
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67 in_type executable myrimatch_executable \ |
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68 fido_executable fidocp_executable \ |
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69 omssa_executable pepnovo_executable \ |
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70 xtandem_executable param_model_directory \ |
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71 java_executable java_memory java_permgen \ |
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72 r_executable rt_concat_trafo_out \ |
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73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ |
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74 -s PATH/TO/SKIP_TOOLS_FILES.txt |
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75 ``` |
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76 |
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77 |
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78 * 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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79 |
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80 ``` |
2
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81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml |
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82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml |
0
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83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml |
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84 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml |
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85 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml |
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86 ``` |
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87 |
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88 * 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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89 |
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90 ``` |
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91 <command><![CDATA[ |
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92 |
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93 ## check input file type |
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94 #set $in_type = $param_in.ext |
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95 |
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96 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files |
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97 ln -s '$param_in' 'param_in.${in_type}' && |
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98 ln -s '$param_database' param_database.fasta && |
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99 ## find location of the MSGFPlus.jar file of the msgf_plus conda package |
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100 MSGF_JAR=\$(msgf_plus -get_jar_path) && |
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101 |
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102 MSGFPlusAdapter |
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103 -executable \$MSGF_JAR |
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104 #if $param_in: |
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105 -in 'param_in.${in_type}' |
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106 #end if |
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107 #if $param_out: |
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108 -out $param_out |
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109 #end if |
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110 #if $param_mzid_out: |
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111 -mzid_out $param_mzid_out |
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112 #end if |
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113 #if $param_database: |
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114 -database param_database.fasta |
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115 #end if |
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116 |
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117 [...] |
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118 ]]> |
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119 ``` |
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120 |
2
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121 * In `MetaProSIP.xml` add `R` as a requirement: |
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122 |
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123 ``` |
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124 <expand macro="requirements"> |
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125 <requirement type="package" version="3.3.1">r-base</requirement> |
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126 </expand> |
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127 ``` |
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128 |
1
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129 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): |
0
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130 |
1
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131 ``` |
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132 <command><![CDATA[ |
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133 |
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134 ## check input file type |
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135 #set $in_type = $param_in.ext |
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136 |
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137 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files |
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138 ln -s '$param_in' 'param_in.${in_type}' && |
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139 |
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140 IDFileConverter |
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141 |
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142 #if $param_in: |
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143 -in 'param_in.${in_type}' |
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144 #end if |
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145 |
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146 [...] |
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147 ]]> |
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148 ``` |
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149 |
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150 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: |
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151 |
1
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152 - `<data name="param_out" auto_format="true"/>` |
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153 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` |
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154 |
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155 * 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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156 |
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157 ``` |
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158 <tests> |
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159 <test> |
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160 <param name="param_in" value="DecoyDatabase_input.fasta"/> |
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161 <output name="param_out" file="DecoyDatabase_output.fasta"/> |
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162 </test> |
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163 </tests> |
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164 ``` |
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165 |
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166 |
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167 * 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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168 * SeedListGenerator |
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169 * SpecLibSearcher |
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170 * MapAlignerIdentification |
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171 * MapAlignerPoseClustering |
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172 * MapAlignerSpectrum |
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173 * MapAlignerRTTransformer |
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174 |
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175 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: |
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176 * OMSSAAdapter |
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177 * MyrimatchAdapter |
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178 |
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179 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: |
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180 * PepNovoAdapter |
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181 |
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182 |
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183 Licence (MIT) |
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184 ============= |
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185 |
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186 Permission is hereby granted, free of charge, to any person obtaining a copy |
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187 of this software and associated documentation files (the "Software"), to deal |
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188 in the Software without restriction, including without limitation the rights |
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189 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
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190 copies of the Software, and to permit persons to whom the Software is |
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191 furnished to do so, subject to the following conditions: |
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192 |
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193 The above copyright notice and this permission notice shall be included in |
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194 all copies or substantial portions of the Software. |
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195 |
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196 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
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197 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
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198 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
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199 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
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200 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
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201 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN |
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202 THE SOFTWARE. |
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203 |