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Table of Contents
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
- Version: 1.17.07.26
- Added: July, 2017
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 $PREFIX/flapjack.jar "$@"