Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

diff phylogenies/beast.sh @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/beast.sh	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Helper script to change output file names then run BEAST.
+
+# Usage: ./beast.sh STDOUT_LOG XMLCONFIG BEAGLESSE
+
+newxml=$(python26 /home/galaxy/galaxy-dist/tools/osiris/phylogenies/beast.py ${2} $(pwd))
+java -jar -Xms4096m -Xmx8192m /home/galaxy/pkgs/BEAST172/lib/beast.jar -overwrite ${3} -threads 8 ${newxml} > ${1} 2>&1