diff bin/batchqsub.pl_orig @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/batchqsub.pl_orig	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,158 @@
+
+# modified from Chenghai Xue's script
+
+#test if qsub works
+
+my $qsub_checker = 0;
+if(system("hash qsub >/dev/null"))
+{
+	$qsub_checker = 0;
+}
+else
+{
+	$test_randname=random_sessid();
+	system("mkdir $test_randname;");
+	system("echo 'mkdir $test_randname/$test_randname' >$test_randname/$test_randname.sh");
+	system("mkdir $test_randname/qsub_cache");
+	system ("qsub -cwd -v TMPDIR=$test_randname/qsub_cache -V -e $test_randname/qsub_cache -o $test_randname/qsub_cache -N $test_randname  $test_randname/$test_randname.sh");
+
+	$status=0;
+	$sec=5;
+	while(1)
+	{
+		$chkresult=`qstat |grep $test_randname |wc -l`;
+		chomp($chkresult);
+		if ($chkresult == 0)
+		{
+			$sec=10;
+			$status++;
+			last if ($status==3);
+		}
+		else
+		{
+			$status=0;
+			$sec=5;
+		}
+		print "QSTAT: $chkresult testing tasks running.....$taskname\n";
+		sleep($sec);
+	}
+	print "QSUB: testing done\n";
+	print "$test_randname/$test_randname\n";
+	if(-d "$test_randname/$test_randname")
+	{
+		$qsub_checker=1;
+		print "QSUB: working well!\n";
+	}
+#$qsub_checker=`qsub </dev/null 2>&1|grep stdin|wc -l`;
+	system("rm $test_randname -rf");
+}
+#$qsub_checker=0;
+if($qsub_checker == 0)
+{
+	print "QSUB: No GRID qsub found\n";
+	print "QSUB: if you are using PBS qsub, please wait for the next version! Thanks.\n";
+	print "QSUB: Running in serial mode...\n";
+	system("sh $ARGV[0]");
+	exit;
+}
+
+$performListFile = $ARGV[0];
+$taskname = "";
+$taskname = $ARGV[1];
+if (not $taskname)
+{
+	$taskname=random_sessid();
+}
+#$outfullDir = $ARGV[2];
+$outfullDir ="qsub_cache";
+
+# correct path
+if(! (-d $outfullDir) ){
+	system ("mkdir $outfullDir");
+}
+
+# create a temp cache
+@temp = split("/", $0);
+$prog = pop @temp;
+$cache = $outfullDir."/".$prog."_".$taskname;
+if(! (-d $cache) ){
+	system ("mkdir $cache");
+}
+
+open (IN_1, "$performListFile") or die "can not open file $performListFile to read\n";
+@performList = (<IN_1>);
+chomp @performList;
+close IN_1 or die "can't close the input file : $!";
+
+
+$scriptListFile = $outfullDir."/".$taskname."_scripts.list";
+open (FSCRIPLIST, ">$scriptListFile");
+for($i=0; $i<@performList; $i++){
+	$scriptFile = $outfullDir."/".$taskname."_script$i.sh";
+	print FSCRIPLIST "$scriptFile\n";
+	open (FOUT, ">$scriptFile");
+
+#	print FOUT "#!/usr/bin/sh\n";
+	print FOUT "$performList[$i]\n";
+			
+#		print OUT_1 "$outfile.map\n";
+	close (FOUT);
+}
+close (FSCRIPLIST);
+
+open (IN_2, "$scriptListFile") or die "can not open file $scriptListFile to read\n";
+$basename=`basename $performListFile`;
+chop($basename);
+$taskname=$taskname."_".$basename;
+#print $basename;
+while(<IN_2>){
+	$f = $_;
+	chomp $f;
+	@temp = split("/", $f);
+	$base = pop @temp;
+	
+	#use default queues
+#	print "/opt/n1ge6/bin/lx24-amd64/qsub -l virtual_free=1.7G -cwd -v TMPDIR=$cache -V -e $cache -o $cache -N $taskname.$base $f\n\n\n";
+	#system ("qsub -l virtual_free=1.7G -cwd -v TMPDIR=$cache -V -e $cache -o $cache -N $taskname.$base $f");
+	system ("qsub -cwd -v TMPDIR=$cache -V -e $cache -o $cache -N $taskname.$base $f");
+	
+}
+close IN_2 or die "can't close the input file : $!";
+
+#start to check stats of qsub tasks
+#######################################
+my $taskname_query=substr($taskname,0,10);
+
+
+$status=0;
+$sec=60;
+while(1)
+{
+	$chkresult=`qstat |grep $taskname_query |wc -l`;
+	chomp($chkresult);
+	if ($chkresult == 0)
+	{
+		$sec=10;
+		$status++;
+		last if ($status==3);
+	}
+	else
+	{
+		$status=0;
+		$sec=60;
+	}
+	print "QSTAT: $chkresult tasks running.....$taskname\n";
+	sleep($sec);
+}
+print "QSUB: done: $taskname \n";
+######################################
+
+#
+sub random_sessid
+{
+	#my @chars = (0..9,a..z,A..Z);
+	my @chars = ('a'..'z','A'..'Z');
+	my $len = 10;
+	my $string = join '', map {$chars[rand(@chars)]} (1..$len);
+	return $string;
+}