Mercurial > repos > galaxyp > openms_rtpredict
comparison readme.md @ 2:4a234c7264e1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
| author | galaxyp |
|---|---|
| date | Wed, 18 Oct 2017 15:43:33 -0400 |
| parents | ad805b03ddf8 |
| children | 6c89e2d9a008 |
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| 1:ad805b03ddf8 | 2:4a234c7264e1 |
|---|---|
| 67 in_type executable myrimatch_executable \ | 67 in_type executable myrimatch_executable \ |
| 68 fido_executable fidocp_executable \ | 68 fido_executable fidocp_executable \ |
| 69 omssa_executable pepnovo_executable \ | 69 omssa_executable pepnovo_executable \ |
| 70 xtandem_executable param_model_directory \ | 70 xtandem_executable param_model_directory \ |
| 71 java_executable java_memory java_permgen \ | 71 java_executable java_memory java_permgen \ |
| 72 r_executable rt_concat_trafo_out \ | |
| 72 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ | 73 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ |
| 73 -s PATH/TO/SKIP_TOOLS_FILES.txt | 74 -s PATH/TO/SKIP_TOOLS_FILES.txt |
| 74 ``` | 75 ``` |
| 75 | 76 |
| 76 | 77 |
| 77 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: | 78 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: |
| 78 | 79 |
| 79 ``` | 80 ``` |
| 80 sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml | 81 sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml |
| 81 sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml | 82 sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml |
| 82 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml | 83 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml |
| 83 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml | 84 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml |
| 84 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml | 85 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml |
| 85 ``` | 86 ``` |
| 86 | 87 |
| 115 | 116 |
| 116 [...] | 117 [...] |
| 117 ]]> | 118 ]]> |
| 118 ``` | 119 ``` |
| 119 | 120 |
| 121 * In `MetaProSIP.xml` add `R` as a requirement: | |
| 122 | |
| 123 ``` | |
| 124 <expand macro="requirements"> | |
| 125 <requirement type="package" version="3.3.1">r-base</requirement> | |
| 126 </expand> | |
| 127 ``` | |
| 128 | |
| 120 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): | 129 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): |
| 121 | 130 |
| 122 ``` | 131 ``` |
| 123 <command><![CDATA[ | 132 <command><![CDATA[ |
| 124 | 133 |