Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository gemini_load
Name: gemini_load
Owner: iuc
Synopsis: Wrapper for the gemini tool suite: GEMINI load
The intent of GEMINI (GEnome MINIing) is to provide a simple, flexible, and powerful framework for exploring genetic variation for
personal and medical genetics. GEMINI is unique in that it integrates genetic variation (from VCF files) with a wealth of genome
annotations into a unified database framework. Using this integrated database as the analysis framework, we aim to leverage the
expressive power of SQL for data analysis, while attempting to overcome the fundamental challenges associated with using databases for
very large (e.g. 1,000,000 variants times 1,000 samples yields one billion genotypes) datasets. In addition, by defining sample
relationships with a PED file, GEMINI allows one to explore and test for variants that meet specific inheritance models (e.g.,
recessive, dominant, etc.).
Type: unrestricted
Revision: 6:b2c25142267e
This revision can be installed: True
Times cloned / installed: 571

Repository README files - may contain important installation or license information

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.

System Message: WARNING/2 (<string>, line 16); backlink

Inline emphasis start-string without end-string.

Note

If the version of GEMINI that you are upgrading to uses a gemini-config.yaml file that is different from the one found in test-data/test-cache you will have to upgrade this file manually (make sure you leave the line annotation_dir: gemini/data unchanged in the process).

Dependencies of this repository

Repository data_manager_gemini_database_downloader revision f57426daa04d owned by iuc

Contents of this repository

Name Description Version Minimum Galaxy Version
Loading a VCF file into GEMINI 0.20.1+galaxy1 16.01

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data