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1 #!/usr/bin/perl
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2
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3 use File::Temp qw/ tempfile tempdir /;
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4 use File::Copy qw/ copy /;
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5 use Cwd;
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6
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7 $mirna_file = $ARGV[0];
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8 $trans_file = $ARGV[1];
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9 $targets = $ARGV[2];
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10
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11 # do all the dirty work in a temp directory
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12 $cwd = cwd();
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13 $tempdir = tempdir(CLEANUP => 1);
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14
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15 copy ("/data/galaxy/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/nikhil-joshi/mirdeep2_and_targetspy/798fe7ba8b5e/mirdeep2_and_targetspy/mirdeep2/target_spy_wrapper.sh", $tempdir);
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16 chdir ($tempdir);
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17
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18 $ret_ts = `sh target_spy_wrapper.sh $mirna_file $trans_file`;
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19 if ($ret_ts ne "") {die "TargetSpy error"}
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20 copy ("targets", $targets);
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21
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22 chdir($cwd);
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