Mercurial > repos > crs4 > edena
comparison 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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| 1:cd6cc6d76708 | 2:b8c6a38530eb |
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| 1 Edena wrapper | |
| 2 ============= | |
| 3 | |
| 4 Configuration | |
| 5 ------------- | |
| 6 | |
| 7 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 ). | |
| 8 | |
| 9 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. | |
| 10 | |
| 11 If instead you are using an older Galaxy release, you should also add a line | |
| 12 | |
| 13 GALAXY_SLOTS=N; export GALAXY_SLOTS | |
| 14 | |
| 15 (where N is the number of CPU cores allocated by the job runner for this tool) to the file | |
| 16 | |
| 17 <tool_dependencies_dir>/edena/3.131028/crs4/edena/<hash_string>/env.sh | |
| 18 | |
| 19 Version history | |
| 20 --------------- | |
| 21 | |
| 22 - 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 . | |
| 23 - Release 1: Simplify passing repeated params to Python script. Add more info to help sections. | |
| 24 - Release 0: Initial release in the Tool Shed. | |
| 25 | |
| 26 Development | |
| 27 ----------- | |
| 28 | |
| 29 Development is hosted at https://bitbucket.org/crs4/orione-tools . Contributions and bug reports are very welcome! |