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annotate readme.rst @ 0:269c40fdcccb draft

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author iuc
date Thu, 18 Feb 2016 08:55:06 -0500
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1 =========================
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2 Galaxy wrapper for GEMINI
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3 =========================
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6 GEMINI: a flexible framework for exploring genome variation
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8 GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of
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9 the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes,
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10 and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very
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11 powerful system for exploring genetic variation for for disease and population genetics.
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13 Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically
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14 annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks,
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15 OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows
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16 one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an
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17 enhanced SQL engine.
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19 Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153).
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22 ============
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23 Installation
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24 ============
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26 It is recommended to install this wrapper via the `Galaxy Tool Shed`.
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28 .. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini
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31 =======
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32 History
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33 =======
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34 - 0.9.1: Initial public release
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37 ====================
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38 Detailed description
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39 ====================
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41 View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html
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44 ===============================
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45 Wrapper Licence (MIT/BSD style)
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46 ===============================
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48 Permission to use, copy, modify, and distribute this software and its
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49 documentation with or without modifications and for any purpose and
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50 without fee is hereby granted, provided that any copyright notices
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51 appear in all copies and that both those copyright notices and this
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52 permission notice appear in supporting documentation, and that the
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53 names of the contributors or copyright holders not be used in
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54 advertising or publicity pertaining to distribution of the software
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55 without specific prior permission.
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57 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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58 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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59 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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60 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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61 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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62 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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63 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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64 OR PERFORMANCE OF THIS SOFTWARE.
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