Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

diff alignment/prottest_wrapper.pl @ 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/alignment/prottest_wrapper.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,16 @@
+#!/usr/bin/perl
+
+use warnings;
+use strict;
+use Cwd;
+
+my $dir=getcwd();
+
+#protest directory placed in main user path.  Also, changed runProttest
+#script to include full path of jar file
+my $prottestPath='/home/galaxy/pkgs/ProtTest2.4';
+
+my $input=$ARGV[1];
+my $output=$ARGV[3];
+
+system "$prottestPath/runProtTest -i $input -o $output" ;