Mercurial > repos > edward-kirton > roche454_toolsuite

comparison runMapping_cDNA_wrapper.pl @ 3:bf1f8bc4abe6 default tip

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minor updates for v2.6
author eskirton@lbl.gov
date Wed, 21 Dec 2011 19:42:53 -0800
parents 2d86d5b112e8
children
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2:2d86d5b112e8 3:bf1f8bc4abe6
34 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED 34 # REMOVE PARAMETERS FOR OPTIONAL FILES WHICH WERE NOT PROVIDED
35 35
36 my @cmd=removeUnusedOptions(@ARGV); 36 my @cmd=removeUnusedOptions(@ARGV);
37 37
38 # RUN COMMAND 38 # RUN COMMAND
39 # NOTE: FIRST ARG EXPECTED TO BE EXECUTABLE
40 my $stderr; 39 my $stderr;
41 eval { $stderr=`@cmd 2>&1`; }; 40 eval { $stderr=`runMapping @cmd 2>&1`; };
42 if ( $@ ) { 41 if ( $@ ) {
43 print STDERR "Newbler ERROR: $stderr\n"; 42 print STDERR "Newbler ERROR: $stderr\n";
44 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`; 43 `cat $outdir/assembly/454NewblerProgress.txt 1>&2`;
45 die($@); 44 die($@);
46 } 45 }