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flapjack-software [2017/07/25 10:17]
aorth created
flapjack-software [2018/04/24 07:46] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 1.16.10.31+  * Version: 1.18.04.23-beta
   * Added: July, 2017   * Added: July, 2017
 +  * Updated: April, 2018
   * Link: https://ics.hutton.ac.uk/flapjack/   * Link: https://ics.hutton.ac.uk/flapjack/
  
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 Load and run flapjack: Load and run flapjack:
-<code>$ module load flapjack/1.16.10.31+<code>$ module load flapjack/1.18.04.23-beta
 $ flapjack</code> $ 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 [[command line documentation for more information|http://flapjack.hutton.ac.uk/en/latest/command_line_support.html]].+**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 ====== ===== Installation ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget http://bioinf.hutton.ac.uk/flapjack/installers/flapjack_linux_x64_1_16_10_31.sh +$ 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_16_10_31.sh +$ chmod +x flapjack_linux_x64_1_18_04_23-BETA.sh 
-$ ./flapjack_linux_x64_1_16_10_31.sh -c -dir /tmp/flapjack +$ sudo mkdir -p /export/apps/flapjack/1.18.04.23-beta 
-$ sudo mkdir -p /export/apps/flapjack/1.16.10.31 +$ sudo chown aorth /export/apps/flapjack/1.18.04.23-beta 
-$ sudo cp flapjack/lib//export/apps/flapjack/1.16.10.31 +$ ./flapjack_linux_x64_1_18_04_23-BETA.sh -c -dir 
-$ sudo chown -R root:root /export/apps/flapjack/1.16.10.31</code> +$ sudo chown -R root:root /export/apps/flapjack/1.18.04.23-beta</code>
- +
-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: +
-<code>#!/usr/bin/env bash +
- +
-readonly PREFIX=$(dirname $0) +
- +
-java -cp $PREFIX/flapjack.jar jhi.flapjack.io.cmd.CreateProject "$@"</code>+
flapjack-software.1500977864.txt.gz · Last modified: 2017/07/25 10:17 by aorth