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flapjack-software

Flapjack

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.

Information

Usage

See versions of flapjack which are available:

$ module avail flapjack

Load and run flapjack:

$ module load flapjack/1.17.07.26
$ 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 command line documentation for more information.

Installation

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 -jar $PREFIX/flapjack.jar "$@"
flapjack-software.txt · Last modified: 2017/07/26 13:43 by aorth