Mercurial > repos > galaxyp > openms_multiplexresolver
comparison readme.md @ 2:900976d81ed2 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 15:37:40 -0400 |
parents | 7268379f9860 |
children | 67abac9bce4f |
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1:7268379f9860 | 2:900976d81ed2 |
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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 |