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Repository gemini_set_somatic

Name: gemini_set_somatic

Owner: iuc

Synopsis: Wrapper for the gemini tool suite: GEMINI set_somatic

Detailed description:

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.).

Content homepage: https://github.com/arq5x/gemini

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/gemini_set_somatic/7b031989ea12

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/gemini_set_somatic

Type: unrestricted

Revision: 4:7b031989ea12

This revision can be installed: True

Times cloned / installed: 1017

Repository README files - may contain important installation or license information

Readme files

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. .. 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).

Contents of this repository

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
GEMINI set_somatic View tool metadata	Tag somatic mutations in a GEMINI database	0.18.1.1	16.01