# HG changeset patch # User galaxyp # Date 1508353806 14400 # Node ID 797d5c59ef5bb7996ccd1e1c2273a6950363e176 # Parent 974dec16eb84ee1cbe40ab6a4602bb8dd5946728 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64 diff -r 974dec16eb84 -r 797d5c59ef5b macros.xml --- a/macros.xml Wed Aug 09 08:58:14 2017 -0400 +++ b/macros.xml Wed Oct 18 15:10:06 2017 -0400 @@ -6,6 +6,7 @@ xtandem fido msgf_plus + diff -r 974dec16eb84 -r 797d5c59ef5b readme.md --- a/readme.md Wed Aug 09 08:58:14 2017 -0400 +++ b/readme.md Wed Oct 18 15:10:06 2017 -0400 @@ -69,6 +69,7 @@ omssa_executable pepnovo_executable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ + r_executable rt_concat_trafo_out \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ -s PATH/TO/SKIP_TOOLS_FILES.txt ``` @@ -77,8 +78,8 @@ * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: ``` - sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml - sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml + sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml @@ -117,6 +118,14 @@ ]]> ``` + * In `MetaProSIP.xml` add `R` as a requirement: + + ``` + + r-base + + ``` + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): ``` diff -r 974dec16eb84 -r 797d5c59ef5b repository_dependencies.xml --- a/repository_dependencies.xml Wed Aug 09 08:58:14 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - -