These HOMER suite is copyright 2013 by Björn Grüning.
See the licence text below.
Version | Changes |
v0.0.1 |
HOMER is bundled with many additional data and it seems not easy to me to split the HOMER source and the data into different packages. That means that we can't install the HOMER program from the Tool Shed. What means we are loosing reproducibility.
To solve that issue I would recommend to install HOMER manually following the instructions from the HOMER website:
http://biowhat.ucsd.edu/homer/introduction/install.html
Installing the required 3rd Party Software is _not_ necessary. We will install it through the Galaxy Tool Shed.
If you install every update of HOMER and/or its data files into a new folder from scratch, you can preserve reproducibility. The HOMER wrapper will locate every single HOMER installation mentioned in a config file (homer.loc) and will use only one specific version (and its data). With that trick we are flexible without changing to much in HOMER and reproducible at the same time.
- install HOMER manually in a special folder and download all required data files
- install the HOMER wrappers from the Tool Shed
- edit the GALXY_ROOT/tool-data/homer.loc file and point to your different HOMER installations
- edit the GALXY_ROOT/tool-data/homer_available_genomes.loc file and add genome identifiers (e.g. hg19, mm9)
Normally you would install this via the Galaxy ToolShed, which would move the provided homer.py file into a suitable location and process the datatypes_conf.xml entry to be combined with your local configuration.
However, if you really want to this should work for a manual install. Add the following lines to the datatypes_conf.xml file in the Galaxy main folder:
<datatype extension="homer_tagdir" type="galaxy.datatypes.homer:TagDirectory" mimetype="text/html" display_in_upload="false"/>
Also create the file lib/galaxy/datatypes/homer.py by moving, copying or linking the homer.py file provided in this tar-ball. Finally add 'import homer' near the start of file lib/galaxy/datatypes/registry.py (after the other import lines).
You can file an issue here https://github.com/bgruening/galaxytools/issues or ask us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
Development is happening here:
https://github.com/bgruening/galaxytools/
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
NOTE: This is the licence for the Galaxy HOMER datatypes only. HOMER and associated data files are available and licenced separately.