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.

• Version: 1.16.10.31
• Added: July, 2017
• Link: https://ics.hutton.ac.uk/flapjack/

See versions of flapjack which are available:

$ module avail flapjack

Load and run flapjack:

$ module load flapjack/1.16.10.31
$ 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 http://flapjack.hutton.ac.uk/en/latest/command_line_support.html.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://bioinf.hutton.ac.uk/flapjack/installers/flapjack_linux_x64_1_16_10_31.sh
$ chmod +x flapjack_linux_x64_1_16_10_31.sh
$ ./flapjack_linux_x64_1_16_10_31.sh -c -dir /tmp/flapjack
$ sudo mkdir -p /export/apps/flapjack/1.16.10.31
$ sudo cp flapjack/lib/* /export/apps/flapjack/1.16.10.31
$ sudo chown -R root:root /export/apps/flapjack/1.16.10.31

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.

/export/apps/flapjack/1.16.10.31/flapjack:

#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -cp $PREFIX/flapjack.jar jhi.flapjack.io.cmd.CreateProject "$@"