Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

view 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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#!/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" ;