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Repository gemini_pathways
Owner: iuc
Synopsis: Wrapper for the gemini tool suite: GEMINI pathways
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: 4:69b5327a1f88
This revision can be installed: True
Times cloned / installed: 939

Repository README files - may contain important installation or license information

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 ```` 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 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).
Dependencies of this repository

Repository data_manager_gemini_database_downloader revision b4b2b284230a owned by iuc

Contents of this repository

Name Description Version Minimum Galaxy Version
Map genes and variants to KEGG pathways 16.01

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