Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison alignment/jmodeltest.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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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5 use Cwd;
6
7 my $jmodeltest_path = '/home/galaxy/pkgs/jmodeltest';
8 my $jmodeltest_tool = '/home/galaxy/galaxy-dist/tools/jmodeltest';
9
10 my $galaxyPath = getcwd();
11
12 my $input = $ARGV[0];
13 my $likelihoodStyle = $ARGV[1];
14 my $likelihood = $ARGV[2];
15 my $criterion = $ARGV[3];
16 my $extension = $ARGV[4];
17
18 # open increment file
19 open my $file, '<', $jmodeltest_tool."\/increment.txt";
20 my $increment = <$file>;
21 $increment = int($increment);
22 close $file;
23
24 # get the current increment
25 my $temp = $increment;
26
27 # update the increment
28 open(UPDATE, '>'.$jmodeltest_tool."\/increment.txt");
29 $increment = $increment + 1;
30 print UPDATE $increment;
31 close(UPDATE);
32
33 chdir("$jmodeltest_path");
34
35 if($likelihoodStyle eq "-t") {
36 #only need to copy input file
37 qx/cp $input input.$temp.$extension/;
38
39 #print qx/ls/;
40
41 qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle $likelihood -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;
42 qx/rm input.$temp.*/;
43 }
44 elsif($likelihoodStyle eq "-u") {
45 #copy input file
46 qx/cp $input input.$temp.$extension/;
47 #copy likelihood tree
48 qx/cp $likelihood likelihood.$temp.tre/;
49 qx/java -jar jModelTest.jar -d input.$temp.$extension $likelihoodStyle likelihood.$temp.tre -$criterion > $galaxyPath\/output.txt 2> $galaxyPath\/err_log.txt/;
50
51 # clean up
52 qx/rm input.$temp.*/;
53 qx/rm likelihood.$temp.tre/;
54
55 }
56
57 chdir("$galaxyPath");