ls -d1 */shrink* | perl -ne 'my $script = "../tools/run_penGDT_rob.tmp.sh"; chomp; chop; /^(.*?)\/shrink\_(.*?)$/ || die "Weird directory name : $_\n"; my $targ=$1; my $fac=$2; my $dir=$_; my @qpdbs = glob("../../target_domains\/$targ\/$targ*.pdb"); if($#qpdbs==0) { $qpdb=$qpdbs[0]; } else { $qpdb = "../../target_domains\/$targ\/$targ\.1\.pdb"; } @qpath=split /\//, $qpdb; $qname=$qpath[$#
qpath];  `cp ../tools/templ.sh $script; cp $qpdb $dir; echo "cd $dir" >> $script`;  my @spdbs = glob("$dir\/*\.$fac\.pdb");  for $spdb(@spdbs) { $spdb =~ /^$dir\/(.*?)$/ || die "Weird subj name $spdb\n"; my $sname=$1; my $fout = "$qname\_$sname\.tr\.dat"; my $cmd = "../../../../tools/lga_out_2_newGDTTS_uniformcuts_noneighb_1.pl -m $sname -t $qname  -o $fout -rundir ./ >& runpen\_$sname\.log"; `echo "$cmd" >> $script`; } `qsub $script`; ' &