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annotate baseline_wrapper.pl @ 27:0bf826f62f04 default tip

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fixed toolshed not filling fields
author Franco Caramia <franco.caramia@petermac.org>
date Wed, 04 Jun 2014 11:04:17 +1000
parents 2770f49cb0dc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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Franco Caramia <franco.caramia@petermac.org>
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1 #sshpass -p pmac1512 ssh -o StrictHostkeyChecking=no galaxy@pmc-bioinf03 "gmt music play $*"
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2 #echo "gmt music play $*"
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3
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4
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Franco Caramia <franco.caramia@petermac.org>
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5 use strict;
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6 use warnings;
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Franco Caramia <franco.caramia@petermac.org>
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7 use File::Basename;
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Franco Caramia <franco.caramia@petermac.org>
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8 use Cwd;
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Franco Caramia <franco.caramia@petermac.org>
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9 die qq(
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10 Bad numbr of inputs
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11
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12 ) if(!@ARGV);
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14
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15 my $player_options = "";
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16 my $baseline_output;
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17
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18 my $dir = getcwd;
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Franco Caramia <franco.caramia@petermac.org>
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19 my $variable = "";
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Franco Caramia <franco.caramia@petermac.org>
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20 my $files = "";
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21 foreach my $input (@ARGV)
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22 {
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23 my @tmp = split "::", $input;
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24
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25 if($tmp[0] eq "PLAYEROPTION")
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26 {
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27 $variable = $tmp[1];
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28 $variable =~ s/=/ /g;
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29 $player_options = "$player_options $variable";
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30 }
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31 elsif($tmp[0] eq "BASELINEOUTPUT")
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32 {
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33 $baseline_output = $tmp[1];
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34 }
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35 elsif($tmp[0] eq "BAMLISTENTRY")
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36 {
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37 $files = "$files ${tmp[1]}";
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38 }
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39 else
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40 {
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41 die("Unknown Input: $input\n");
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42 }
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43 }
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44
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45
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46 my $working_dir = "BASELINE_OUTPUT";
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47 #remove extension
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48
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49 #Create Contra Output dir
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50 system ("mkdir $working_dir");
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51
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52 #run baseline
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53
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54 system ("baseline.py --file $files --output $working_dir $player_options > /dev/null");
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55
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56 #Search control file in output dir
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57 opendir(DIR, $working_dir);
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58 my @FILES= readdir(DIR);
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59 foreach my $file (@FILES)
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60 {
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61 my ($filename,$directory,$extension) = fileparse($file, qr/\.[^.]*/);
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62 if ($extension eq ".txt")
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63 {
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64 system ("mv $working_dir/$file $baseline_output");
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65 }
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66 }
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67 closedir(DIR);
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68