diff galaxy-tools/tools/rdock/bin/run_rbdock.pl @ 2:0faa03a92843 draft default tip

Uploaded

--- a/galaxy-tools/tools/rdock/bin/run_rbdock.pl	Fri Aug 26 09:55:15 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-#!/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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