Mercurial > repos > iuc > gemini_set_somatic
comparison readme.rst @ 0:230c975e7759 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
| author | iuc |
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| date | Thu, 18 Feb 2016 08:57:23 -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 |