genie

GEnomic Integrated suitE

INSTRUCTIONS FOR GENOME.DK USERS

Installation

first download and install latest Miniconda package (don't source from /com/extra/Anaconda..)

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Just accept the defaults

after installing miniconda,

open a new window and type conda --version and see if you have version > 4.0

then install genie by downloading the installer script

wget https://raw.githubusercontent.com/drveera/genie/master/library/ipsych_installer.sh
sh ipsych_installer.sh

open a new window and type

source activate genie

and you'll be good to go. Type genie -h and you'll see help message like this.

genie

usage:
 genie <command> [<args>...]

The following commands are available:
COMMAND   DESCRIPTION
gwas      run gwas
geneset   run gene/geneset analysis using gwas summary file
rohs      run analysis of runs of homozygosity
prs       run polygenic risk score analysis
gcta      run GCTA analyses

See 'genie <command> --help' for more information on a specific command.
For example, type 'genie geneset --help'