Mercurial > repos > marpiech > norwich_tools_docking

comparison tools/rdock/bin/run_rbdock.pl @ 3:b02d74d22d05 draft default tip

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planemo upload
author marpiech
date Mon, 29 Aug 2016 08:23:52 -0400
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2:bd50f811878f 3:b02d74d22d05
1 #!/usr/bin/perl
2 use lib "$ENV{'RBT_ROOT'}/lib";
3 require "run_rbfuncs.pl";
4
5 my $rbtroot = $ENV{'RBT_ROOT'};
6 my $rbthome = $ENV{'RBT_HOME'};
7 my $recepDir = "$rbtroot/data/receptors";
8 my $scriptDir = "$rbtroot/data/scripts";
9 my $libraryDir = "$rbtroot/data/libraries";
10 my $binDir = "$rbtroot/bin";
11
12 #override default directories
13 #Parse command line arguments
14 my $nArgs = scalar(@ARGV);
15
16 while (scalar(@ARGV)) {
17 my $arg = shift @ARGV;
18 if (index($arg,'-r')==0) {
19 $recepDir = substr($arg,2);
20 }
21 elsif (index($arg,'-s')==0) {
22 $scriptDir = substr($arg,2);
23 }
24 elsif (index($arg,'-l')==0) {
25 $libraryDir = substr($arg,2);
26 }
27 }
28
29
30 # Get the receptor, library and script tables
31 my %receptor_table = get_prm_table($recepDir);
32 my %script_table = get_prm_table($scriptDir);
33 my %library_table = get_prm_table($libraryDir);
34
35 #GET ALL THE INPUTS
36 my $defFiles = "*.{sd,sdf,mol,mdl}";
37 print join("\n",glob $defFiles);
38 my $libFiles = get_input("\n\nEnter expression for SD files to dock",$defFiles);
39 my $receptor = get_selection(\%receptor_table,"receptor");
40 my $script = get_selection(\%script_table,"docking script");
41 my $flags = get_input("Enter optional rbdock flags","-ap -an");
42 my $runs = get_input("Enter number of runs/ligand",20);
43
44 my $runRoot = get_input("Enter run name","rbdock");
45 my $queueSys = get_input("Enter queuing system (NQS,CODINE,CONDOR,NONE)","CONDOR");
46 my $queueName;
47 $queueName = get_input("Enter NQS queue","QRBD") if ($queueSys eq "NQS");
48
49 $pwd = `pwd`;
50 chomp $pwd;
51
52 #WRITE THE NQS SCRIPTS
53
54 #GET THE LIST OF SD FILES TO DOCK
55 my @libList = glob "${libFiles}";
56
57 my $subFile = "submit_$runRoot.csh";
58 open SUBHANDLE,">$subFile";
59 print SUBHANDLE "#!/bin/csh -ef\n";
60
61 my $iFile=0;
62 foreach $libFile (@libList) {
63 $iFile++;
64 #Write the NQS script file
65 $runName = "${runRoot}_$iFile";
66 $nqsFile = "run_${runName}.csh";
67 my $logFile = "${runName}.log";
68
69 print "Writing $nqsFile...\n";
70
71 open NQSHANDLE,">$nqsFile";
72 print NQSHANDLE "#!/bin/csh -ef\n";
73 print NQSHANDLE "setenv RBT_ROOT $rbtroot\n";
74 print NQSHANDLE "setenv RBT_HOME $rbthome\n";
75 print NQSHANDLE "source \$RBT_ROOT/bin/setlibrbt.com\n";
76 print NQSHANDLE "cd $pwd\n";
77 print NQSHANDLE "if (-e $logFile) rm -f $logFile\n";
78 print NQSHANDLE "\$RBT_ROOT/bin/rbdock -i$libFile -o${runName} -r$receptor -p$script -n$runs $flags > $logFile\n";
79 close NQSHANDLE;
80
81 chmod 0755,$nqsFile;
82 print SUBHANDLE "qsub -q $queueName $nqsFile\n" if ($queueSys eq "NQS");
83 print SUBHANDLE "qsub -e $pwd/$runRoot/tmp/ -o $pwd/$runRoot/tmp/ $nqsFile\n" if ($queueSys eq "CODINE");
84 if ($queueSys eq "CONDOR") {
85 my $condorFile = "run_${runName}.cmd";
86 open CMDHANDLE,">$condorFile";
87 print CMDHANDLE "#CONDOR FILE WRITTEN BY run_rbscreen.pl\n";
88 print CMDHANDLE "universe = vanilla\n";
89 print CMDHANDLE "executable = ${nqsFile}\n";
90 print CMDHANDLE "Requirements = CATALYST_NODE =!= True\n";
91 print CMDHANDLE "output = ${nqsFile}.out\n";
92 print CMDHANDLE "error = ${nqsFile}.err\n";
93 print CMDHANDLE "log = ${nqsFile}.log\n";
94 print CMDHANDLE "queue\n";
95 close NQSHANDLE;
96 print SUBHANDLE "condor_submit $condorFile\n";
97 }
98 }
99 close SUBHANDLE;
100 chmod 0755,$subFile;
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