gemini¶

GEMINI (GEnome MINIng) is 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 phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.

Making gemini available¶

The following module command makes the latest version of gemini available to your session:

module load apps/gcc/4.4.7/gemini

Alternatively, you can make a specific version available:

module load apps/gcc/4.4.7/gemini/0.18

Installation notes¶

These are primarily for system administrators.

gemini was installed using the gcc 4.4.7 compiler
install_gemini.sh

Testing¶

The test script used was

test_gemini.sh

The full output from the test run is on the system at /usr/local/packages6/apps/gcc/4.4.7/gemini/0.18/test_results/

There was one failure:

    effstring.t02...\c
ok
    effstring.t03...\c
15d14
< gene    impact  impact_severity biotype is_exonic       is_coding       is_lof
64a64
> gene    impact  impact_severity biotype is_exonic       is_coding       is_lof
fail
updated 10 variants
     annotate-tool.t1 ... ok
updated 10 variants
     annotate-tool.t2 ... ok

This was reported to the developers who indicated that it was nothing to worry about

Modulefile¶

The module file is on the system at /usr/local/modulefiles/apps/gcc/4.4.7/gemini/0.18

The contents of the module file is

#%Module1.0#####################################################################
##
## Gemini module file
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
      global bedtools-version

      puts stderr "   Adds `gemini-$geminiversion' to your PATH environment variable"
}

set     geminiversion 0.18

prepend-path PATH /usr/local/packages6/apps/gcc/4.4.7/gemini/0.18/bin/