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Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes.



See versions of flapjack which are available:

$ module avail flapjack

Load and run flapjack:

$ module load flapjack/
$ flapjack

Note: By default Flapjack is a graphical application—make sure you have logged into HPC with ssh -X before trying to use it. Otherwise, you can use Flapjack's command line utilities like createproject, splitproject, creatematrix, etc. See the


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ chmod +x
$ ./ -c -dir /tmp/flapjack
$ sudo mkdir -p /export/apps/flapjack/
$ sudo cp flapjack/lib/* /export/apps/flapjack/
$ sudo chown -R root:root /export/apps/flapjack/

I created simple wrapper scripts for flapjack and its other command line programs, as they must otherwise be run with java -jar .. or java -cp .. and is rather user-unfriendly.


#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -cp $PREFIX/flapjack.jar "$@"
flapjack-software.1500977864.txt.gz · Last modified: 2017/07/25 10:17 by aorth