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flapjack-software [2017/07/25 13:17]
aorth created
flapjack-software [2018/04/24 10:46] (current)
aorth
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 ===== 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 13:17 by aorth