diff readme.rst @ 0:720cbfb4190d draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,65 @@
+=========================
+Galaxy wrapper for GEMINI
+=========================
+
+
+GEMINI: a flexible framework for exploring genome variation
+
+GEMINI (GEnome MINIng) is designed to be a flexible framework for exploring genetic variation in the context of 
+the wealth of genome annotations available for the human genome. By placing genetic variants, sample genotypes, 
+and useful genome annotations into an integrated database framework, GEMINI provides a simple, flexible, yet very 
+powerful system for exploring genetic variation for for disease and population genetics.
+
+Using the GEMINI framework begins by loading a VCF file into a database. Each variant is automatically 
+annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, 
+OMIM, dbSNP, KEGG, and HPRD. All of this information is stored in portable SQLite database that allows 
+one to explore and interpret both coding and non-coding variation using “off-the-shelf” tools or an 
+enhanced SQL engine.
+
+Please also see the original [manuscript](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003153).
+
+
+============
+Installation
+============
+
+It is recommended to install this wrapper via the `Galaxy Tool Shed`.
+
+.. _`Galaxy Tool Shed`:  https://testtoolshed.g2.bx.psu.edu/view/iuc/gemini
+
+
+=======
+History
+=======
+- 0.9.1: Initial public release
+
+
+====================
+Detailed description
+====================
+
+View the original GEMINI documentation: http://gemini.readthedocs.org/en/latest/index.html
+
+
+===============================
+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.
+