diff galaxy-tools/tools/rdock/bin/run_rbdock.pl @ 0:4eb3f9cb2a51 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/tools/rdock/bin/run_rbdock.pl	Fri Aug 26 09:53:37 2016 -0400
@@ -0,0 +1,116 @@
+#!/usr/bin/perl
+use lib "$ENV{'RBT_ROOT'}/lib";
+require "run_rbfuncs.pl";
+
+my $rbtroot = $ENV{'RBT_ROOT'};
+my $rbthome = $ENV{'RBT_HOME'};
+my $recepDir = "$rbtroot/data/receptors";
+my $scriptDir = "$rbtroot/data/scripts";
+my $libraryDir = "$rbtroot/data/libraries";
+my $binDir = "$rbtroot/bin";
+
+#override default directories
+#Parse command line arguments
+my $nArgs = scalar(@ARGV);
+
+while (scalar(@ARGV)) {
+  my $arg = shift @ARGV;
+  if (index($arg,'-r')==0) {
+      $recepDir = substr($arg,2);
+  }
+  elsif (index($arg,'-s')==0) {
+      $scriptDir = substr($arg,2);
+  }
+  elsif (index($arg,'-l')==0) {
+      $libraryDir = substr($arg,2);
+  }
+}
+
+
+# Get the receptor, library and script tables
+my %receptor_table = get_prm_table($recepDir);
+my %script_table = get_prm_table($scriptDir);
+my %library_table = get_prm_table($libraryDir);
+
+#GET ALL THE INPUTS
+my $defFiles = "*.{sd,sdf,mol,mdl}";
+print join("\n",glob $defFiles);
+my $libFiles = get_input("\n\nEnter expression for SD files to dock",$defFiles);
+my $receptor = get_selection(\%receptor_table,"receptor");
+my $script = get_selection(\%script_table,"docking script");
+my $flags = get_input("Enter optional rbdock flags","-ap -an");
+my $runs = get_input("Enter number of runs/ligand",20);
+
+my $runRoot = get_input("Enter run name","rbdock");
+my $queueSys = get_input("Enter queuing system (NQS,CODINE,CONDOR,NONE)","CONDOR");
+my $queueName;
+$queueName = get_input("Enter NQS queue","QRBD") if ($queueSys eq "NQS");
+
+$pwd = `pwd`;
+chomp $pwd;
+
+#WRITE THE NQS SCRIPTS
+
+#GET THE LIST OF SD FILES TO DOCK
+my @libList = glob "${libFiles}";
+
+my $subFile = "submit_$runRoot.csh";
+open SUBHANDLE,">$subFile";
+print SUBHANDLE "#!/bin/csh -ef\n";
+
+my $iFile=0;
+foreach $libFile (@libList) {
+  $iFile++;
+  #Write the NQS script file
+  $runName = "${runRoot}_$iFile";
+  $nqsFile = "run_${runName}.csh";
+  my $logFile = "${runName}.log";
+
+  print "Writing $nqsFile...\n";
+
+  open NQSHANDLE,">$nqsFile";
+  print NQSHANDLE "#!/bin/csh -ef\n";
+  print NQSHANDLE "setenv RBT_ROOT $rbtroot\n";
+  print NQSHANDLE "setenv RBT_HOME $rbthome\n";
+  print NQSHANDLE "source \$RBT_ROOT/bin/setlibrbt.com\n";
+  print NQSHANDLE "cd $pwd\n";
+  print NQSHANDLE "if (-e $logFile) rm -f $logFile\n";
+  print NQSHANDLE "\$RBT_ROOT/bin/rbdock -i$libFile -o${runName} -r$receptor -p$script -n$runs $flags > $logFile\n";
+  close NQSHANDLE;
+
+  chmod 0755,$nqsFile;
+  print SUBHANDLE "qsub -q $queueName $nqsFile\n" if ($queueSys eq "NQS");
+  print SUBHANDLE "qsub -e $pwd/$runRoot/tmp/ -o $pwd/$runRoot/tmp/ $nqsFile\n" if ($queueSys eq "CODINE");
+  if ($queueSys eq "CONDOR") {
+    my $condorFile = "run_${runName}.cmd";
+    open CMDHANDLE,">$condorFile";
+    print CMDHANDLE "#CONDOR FILE WRITTEN BY run_rbscreen.pl\n";
+    print CMDHANDLE "universe        = vanilla\n";
+    print CMDHANDLE "executable      = ${nqsFile}\n";
+    print CMDHANDLE "Requirements    = CATALYST_NODE =!= True\n";
+    print CMDHANDLE "output          = ${nqsFile}.out\n";
+    print CMDHANDLE "error           = ${nqsFile}.err\n";
+    print CMDHANDLE "log             = ${nqsFile}.log\n";
+    print CMDHANDLE "queue\n";
+    close NQSHANDLE;
+    print SUBHANDLE "condor_submit $condorFile\n";
+  }
+}
+close SUBHANDLE;
+chmod 0755,$subFile;
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