Mercurial > repos > bgruening > repeat_masker
comparison readme.rst @ 0:d4a2c739da3f draft
Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
| author | bgruening |
|---|---|
| date | Tue, 25 Jun 2013 04:33:41 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:d4a2c739da3f |
|---|---|
| 1 =============================== | |
| 2 Galaxy wrapper for RepeatMasker | |
| 3 =============================== | |
| 4 | |
| 5 This wrapper is copyright 2013 by Björn Grüning. | |
| 6 | |
| 7 This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology. | |
| 8 http://www.repeatmasker.org/ | |
| 9 | |
| 10 | |
| 11 Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0. | |
| 12 1996-2010 <http://www.repeatmasker.org>. | |
| 13 | |
| 14 | |
| 15 Additional Information: | |
| 16 Using RepeatMasker to identify repetitive elements in genomic sequences. | |
| 17 http://www.ncbi.nlm.nih.gov/pubmed/19274634 | |
| 18 | |
| 19 ============ | |
| 20 Installation | |
| 21 ============ | |
| 22 | |
| 23 To install RepeatMasker, please use the following instructions: | |
| 24 | |
| 25 http://www.repeatmasker.org/RMDownload.html | |
| 26 | |
| 27 To install the wrapper copy the file RepeatMasker.xml in the galaxy tools | |
| 28 folder and modify the tools_conf.xml file to make the tool available to Galaxy. | |
| 29 Add a line like the following: | |
| 30 | |
| 31 Add the tool definition to your tool_conf.xml file under Galaxy root. | |
| 32 <tool file="RepeatMasker/RepeatMasker.xml" /> | |
| 33 | |
| 34 ======= | |
| 35 History | |
| 36 ======= | |
| 37 | |
| 38 - v1.1: Initial public release | |
| 39 - v0.1.1: patch from Simon Guest, to create empty files if no repeat is found | |
| 40 - v0.1.2: remove trailing semicolon, redirect all output to stdout | |
| 41 | |
| 42 =============================== | |
| 43 Wrapper Licence (MIT/BSD style) | |
| 44 =============================== | |
| 45 | |
| 46 Permission to use, copy, modify, and distribute this software and its | |
| 47 documentation with or without modifications and for any purpose and | |
| 48 without fee is hereby granted, provided that any copyright notices | |
| 49 appear in all copies and that both those copyright notices and this | |
| 50 permission notice appear in supporting documentation, and that the | |
| 51 names of the contributors or copyright holders not be used in | |
| 52 advertising or publicity pertaining to distribution of the software | |
| 53 without specific prior permission. | |
| 54 | |
| 55 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 56 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 57 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 58 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 59 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 60 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 61 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 62 OR PERFORMANCE OF THIS SOFTWARE. | |
| 63 |