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comparison readme.rst @ 0:285f519dab87 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:57:08 -0500
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1 =========================
2 Galaxy wrapper for GEMINI
3 =========================
4
5
6 GEMINI: a flexible framework for exploring genome variation
7
8 GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of
9 the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes,
10 and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very
11 powerful system for exploring genetic variation for for disease and population genetics.
12
13 Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically
14 annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks,
15 OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows
16 one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an
17 enhanced SQL engine.
18
19 Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153).
20
21
22 ============
23 Installation
24 ============
25
26 It is recommended to install this wrapper via the `Galaxy Tool Shed`.
27
28 .. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini
29
30
31 =======
32 History
33 =======
34 - 0.9.1: Initial public release
35
36
37 ====================
38 Detailed description
39 ====================
40
41 View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html
42
43
44 ===============================
45 Wrapper Licence (MIT/BSD style)
46 ===============================
47
48 Permission to use, copy, modify, and distribute this software and its
49 documentation with or without modifications and for any purpose and
50 without fee is hereby granted, provided that any copyright notices
51 appear in all copies and that both those copyright notices and this
52 permission notice appear in supporting documentation, and that the
53 names of the contributors or copyright holders not be used in
54 advertising or publicity pertaining to distribution of the software
55 without specific prior permission.
56
57 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
58 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
59 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
60 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
61 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
62 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
63 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
64 OR PERFORMANCE OF THIS SOFTWARE.
65