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annotate 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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 use warnings;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use Cwd;
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $dir=getcwd();
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #protest directory placed in main user path. Also, changed runProttest
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 #script to include full path of jar file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $prottestPath='/home/galaxy/pkgs/ProtTest2.4';
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12
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13 my $input=$ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $output=$ARGV[3];
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16 system "$prottestPath/runProtTest -i $input -o $output" ;