Differences

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--- flapjack-software [2017/07/25 10:17] – created aorth
+++ flapjack-software [2018/04/24 07:46] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.16.10.31
+  * Version: 1.18.04.23-beta
   * Added: July, 2017
+  * Updated: April, 2018
   * Link: https://ics.hutton.ac.uk/flapjack/
@@ Line 14: / Line 15: @@
 Load and run flapjack:
-<code>$ module load flapjack/1.16.10.31
+<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 [[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 ======
@@ Line 23: / Line 24: @@
 <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>