Mercurial > repos > crs4 > edena
diff readme.rst @ 2:b8c6a38530eb draft default tip
Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA
_SITE_OPTIONS. Directly call edena, remove edena_ovl_wrapper.py and edena_ass_wrapper.py . Discard stderr instead of redirecting to stdout. Do not redirect stdout to logfile. Add readme.rst .
author | crs4 |
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date | Fri, 31 Jan 2014 12:08:21 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Jan 31 12:08:21 2014 -0500 @@ -0,0 +1,29 @@ +Edena wrapper +============= + +Configuration +------------- + +edena_ovl_wrapper tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). + +If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. + +If instead you are using an older Galaxy release, you should also add a line + + GALAXY_SLOTS=N; export GALAXY_SLOTS + +(where N is the number of CPU cores allocated by the job runner for this tool) to the file + + <tool_dependencies_dir>/edena/3.131028/crs4/edena/<hash_string>/env.sh + +Version history +--------------- + +- Release 2: Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA_SITE_OPTIONS. Directly call edena, remove edena_ovl_wrapper.py and edena_ass_wrapper.py . Discard stderr instead of redirecting to stdout. Do not redirect stdout to logfile. Add readme.rst . +- Release 1: Simplify passing repeated params to Python script. Add more info to help sections. +- Release 0: Initial release in the Tool Shed. + +Development +----------- + +Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome!