ILRI Research Computing

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====== 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: 1.18.04.23-beta
  * Added: July, 2017
  * Updated: April, 2018
  * Link: https://ics.hutton.ac.uk/flapjack/

===== Usage =====

See versions of flapjack which are available:
<code>$ module avail flapjack</code>

Load and run flapjack:
<code>$ module load flapjack/1.18.04.23-beta
$ flapjack</code>

**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|command line documentation for more information]].

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://bioinf.hutton.ac.uk/flapjack/gobii-beta/milcah/flapjack_linux_x64_1_18_04_23-BETA.sh
$ chmod +x flapjack_linux_x64_1_18_04_23-BETA.sh
$ sudo mkdir -p /export/apps/flapjack/1.18.04.23-beta
$ sudo chown aorth /export/apps/flapjack/1.18.04.23-beta
$ ./flapjack_linux_x64_1_18_04_23-BETA.sh -c -dir
$ sudo chown -R root:root /export/apps/flapjack/1.18.04.23-beta</code>