Mercurial > repos > bgruening > repeat_masker

annotate readme.rst @ 2:5673e72241aa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 17 Sep 2013 03:23:49 -0400
parents d4a2c739da3f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
1 ===============================
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
2 Galaxy wrapper for RepeatMasker
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
3 ===============================
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
4
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
5 This wrapper is copyright 2013 by Björn Grüning.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
6
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
7 This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
8 http://www.repeatmasker.org/
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
9
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
10
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
11 Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
12 1996-2010 <http://www.repeatmasker.org>.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
13
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
14
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
15 Additional Information:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
16 Using RepeatMasker to identify repetitive elements in genomic sequences.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
17 http://www.ncbi.nlm.nih.gov/pubmed/19274634
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
18
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
19 ============
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
20 Installation
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
21 ============
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
22
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
23 To install RepeatMasker, please use the following instructions:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
24
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
25 http://www.repeatmasker.org/RMDownload.html
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
26
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
27 To install the wrapper copy the file RepeatMasker.xml in the galaxy tools
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
28 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
29 Add a line like the following:
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
30
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
31 Add the tool definition to your tool_conf.xml file under Galaxy root.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
32 <tool file="RepeatMasker/RepeatMasker.xml" />
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
33
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
34 =======
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
35 History
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
36 =======
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
37
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
38 - v1.1: Initial public release
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
39 - v0.1.1: patch from Simon Guest, to create empty files if no repeat is found
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
40 - v0.1.2: remove trailing semicolon, redirect all output to stdout
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
41
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
42 ===============================
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
43 Wrapper Licence (MIT/BSD style)
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
44 ===============================
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
45
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
46 Permission to use, copy, modify, and distribute this software and its
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
47 documentation with or without modifications and for any purpose and
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
48 without fee is hereby granted, provided that any copyright notices
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
49 appear in all copies and that both those copyright notices and this
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
50 permission notice appear in supporting documentation, and that the
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
51 names of the contributors or copyright holders not be used in
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
52 advertising or publicity pertaining to distribution of the software
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
53 without specific prior permission.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
54
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
55 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
56 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
57 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
58 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
59 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
60 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
61 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
62 OR PERFORMANCE OF THIS SOFTWARE.
d4a2c739da3f Initial release under a consistent username. Fixes for stdout and the trailing semicolon.
bgruening
parents:
diff changeset
63