Mercurial > repos > david-hoover > mirdeep2_and_targetspy_dh

comparison target_spy_wrapper.pl @ 0:17e442abb3de draft default tip

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author david-hoover
date Wed, 23 Jul 2014 10:27:07 -0400
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-1:000000000000 0:17e442abb3de
1 #!/usr/bin/perl
2
3 use File::Temp qw/ tempfile tempdir /;
4 use File::Copy qw/ copy /;
5 use Cwd;
6
7 $mirna_file = $ARGV[0];
8 $trans_file = $ARGV[1];
9 $targets = $ARGV[2];
10
11 # do all the dirty work in a temp directory
12 $cwd = cwd();
13 $tempdir = tempdir(CLEANUP => 1);
14
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", $tempdir);
16 chdir ($tempdir);
17
18 $ret_ts = `sh target_spy_wrapper.sh $mirna_file $trans_file`;
19 if ($ret_ts ne "") {die "TargetSpy error"}
20 copy ("targets", $targets);
21
22 chdir($cwd);