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comparison readme.md @ 2:7d0ac73772ea draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:46:01 -0400
parents a4c3db6825f4
children 0b6c969bc55e
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1:a4c3db6825f4 2:7d0ac73772ea
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