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.

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.

Prepare Gemini annotation files and test databases for tool tests

Each version of GEMINI is tied to a particular set of annotation files and database version.

The build-gemini-testdata.sh script in this folder should be used to regenerate the annotation files and the test databases whenever the GEMINI version required by the tool wrappers gets upgraded.

The script requires a working GEMINI installation at the targeted version and a folder with GEMINI's original annotation files, and can be executed with:

sh build-gemini-testdata.sh path/to/gemini/annotation/files

It will regenerate the annotation files inside test-data/test-cache/gemini/data and rebuild the *.db files in test-data.