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 .

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+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!