Mercurial > repos > bgruening > repeat_masker
diff readme.rst @ 0:d4a2c739da3f draft
Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
author | bgruening |
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date | Tue, 25 Jun 2013 04:33:41 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Jun 25 04:33:41 2013 -0400 @@ -0,0 +1,63 @@ +=============================== +Galaxy wrapper for RepeatMasker +=============================== + +This wrapper is copyright 2013 by Björn Grüning. + +This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology. +http://www.repeatmasker.org/ + + +Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0. +1996-2010 <http://www.repeatmasker.org>. + + +Additional Information: +Using RepeatMasker to identify repetitive elements in genomic sequences. +http://www.ncbi.nlm.nih.gov/pubmed/19274634 + +============ +Installation +============ + +To install RepeatMasker, please use the following instructions: + +http://www.repeatmasker.org/RMDownload.html + +To install the wrapper copy the file RepeatMasker.xml in the galaxy tools +folder and modify the tools_conf.xml file to make the tool available to Galaxy. +Add a line like the following: + +Add the tool definition to your tool_conf.xml file under Galaxy root. + <tool file="RepeatMasker/RepeatMasker.xml" /> + +======= +History +======= + +- v1.1: Initial public release +- v0.1.1: patch from Simon Guest, to create empty files if no repeat is found +- v0.1.2: remove trailing semicolon, redirect all output to stdout + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +