ncbi_decrypt: utility script to submit decryption jobs to PBS cluster

ncbi_decrypt

#!/usr/bin/perl

use strict;
use warnings;

my $path = shift @ARGV;
$path ||= $ENV{PWD};

unless ($path =~ m/^\//) {
  $path = "$ENV{PWD}/$path";
}

print "enter decryption password: ";
my $password = <>;
chomp($password);

my @files = `find $path -name \*.ncbi_enc`;

my $jobid;
for my $file (@files) {
  chomp($file);

  my $decrypted = $file;
  $decrypted =~ s/\.ncbi_enc$//;
  next if -e "$decrypted";

  my $backup = "$decrypted~";
  unlink $backup if -e $backup;

  my ($basename) = `basename \Q$file`;
  chomp($basename);
  $basename = "\Q$basename";

  my ($dirname) = `dirname \Q$file`;
  chomp($dirname);
  chdir $dirname or die $!;
  $dirname = "\Q$dirname";

  print "cd $dirname\n";
  print <<EOL;
echo 'cd \$PBS_O_WORKDIR; /h3/t1/apps/genutil/decrypt/decrypt -password $password $basename' | qsub -q cphg -Wgroup_list=CPHG -l select=1:ncpus=1:mem=1GB -l walltime=1:00:00 -W umask=002 -o /dev/null -e /dev/null @{[$jobid ? " -W depend=afterok:$jobid" : '']}
EOL

 ($jobid) = `echo 'cd \$PBS_O_WORKDIR; /h3/t1/apps/genutil/decrypt/decrypt -password $password $basename' | qsub -q cphg -Wgroup_list=CPHG -l select=1:ncpus=1:mem=1GB -l walltime=1:00:00 -W umask=002 -o /dev/null -e /dev/null @{[$jobid ? " -W depend=afterok:$jobid" : '']}`;
 chomp($jobid);
}