debug_messages_2

rp_bin/Ricopili/Version.pm

@@ -15,7 +15,7 @@ our @EXPORT = qw($rp_header $rp_version);
 our ($rp_header, $rp_version);
 
 
-$rp_version = "2018_Nov_30.002" ;
+$rp_version = "2018_Nov_30.005" ;
 
 
 my $rp_logo = <<'END_TXT';

rp_bin/blueprint

@@ -59,6 +59,11 @@ if ($qloc eq "custom") {
     $batch_ncores_per_node = &trans("batch_ncores_per_node");
     $batch_mem_per_node = &trans("batch_mem_per_node");
 }
+else {
+    print "Error: pipeline only runs in custom mode meanwhile\n";
+    print "       please reinstall\n";
+    exit;
+}
 
 
 

rp_bin/my.prepvcf_filtnorm

@@ -104,6 +104,11 @@ if ($chrX) {
 
 my $fasta_file = "$bcrloc/human_g1k_v37.fasta";
 
+unless (-e $fasta_file){
+    print "Error: $fasta_file not existing\n";
+    exit;
+}
+
 my $bcftools2 = $bcloc."bcftools";;
 if ($bcloc =~ / /) {
     $bcftools2 = "bcftools";

rp_bin/my.start_job

@@ -38,7 +38,7 @@ version: $version
       options:
 
         --help           print this message then quit
-        --n INT          line to take as command (like this n100)
+        --n INT          line to take as command (like this 100)
         --jobfile STRING jobfile from which to read command
         --parn INT       number of parallel jobs (then multiplicated with n)
 

rp_bin/refdir_navi

@@ -98,6 +98,7 @@ my $hmloc = &trans("hmloc");
 
 my $email = &trans("email");
 my $loloc = &trans("loloc");
+my $bcrloc = &trans("bcrloc");
 
 #######################################
 
@@ -1523,6 +1524,13 @@ if (@backup_arr > 0) {
 }
 
 
+my $fasta_file = "$bcrloc/human_g1k_v37.fasta";
+
+unless (-e $fasta_file){
+    print "Error: $fasta_file not existing\n";
+    exit;
+}
+
 
 
 foreach my $chrint ($chr_start..$chr_end){

rp_bin/rp_config

@@ -277,17 +277,24 @@ my $command_line = "$progname @ARGV";
 #my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"other",0);
 #my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"computerome",0,"other",0);
 #my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"computerome",0,"co_ipsych",0,"uppmax",0,"other",0);
-my %clusters = ("broad",0,"mssm",0,"genomedk",0,"lisa",0,"computerome",0,"co_ipsych",0,"uppmax",0,"unc_slurm",0,"bih_qsub",0,"custom",0);
-my @cluster_names = ("broad","mssm","genomedk","lisa","computerome","co_ipsych","uppmax","unc_slurm","bih_qsub","custom");
+my %clusters = ("broad_do_not_use",0,"mssm_do_not_use",0,"genomedk_do_not_use",0,"lisa_do_not_use",0,"computerome_do_not_use",0,"co_ipsych_do_not_use",0,"uppmax_do_not_use",0,"unc_slurm_do_not_use",0,"bih_qsub_do_not_use",0,"custom",0);
+my @cluster_names = ("broad_do_not_use","mssm_do_not_use","genomedk_do_not_use","lisa_do_not_use","computerome_do_not_use","co_ipsych_do_not_use","uppmax_do_not_use","unc_slurm_do_not_use","bih_qsub_do_not_use","custom");
+
+
+my $cluster = "custom";
+
+if (0) {
 print "Please enter your cluster environment from the following options:\n";
 print "!!!! since the 1018 versions only custom (10) !!!!!\n";
 my $i = 1;
 foreach (@cluster_names){
-    print "\t($i) $_\n";
+    unless ($_ =~ /do_not_use/) {
+	print "\t($i) $_\n";
+    }
     $i += 1;
 }
 print "\n";
-my $cluster = "other";
+
 while (1) {    
     $cluster = lc <>;
     chomp $cluster;
@@ -307,11 +314,11 @@ while (1) {
 	}
     }
 }
+}
 
-
-print "\nUsing the following cluster: $cluster\n\n";
-
-
+print "\nUsing the following cluster: $cluster\nin combination with $rp_custom_installation_file\n\n";
+sleep (2);
+#exit;
 
 #################################################################################
 ###### CUSTOM configuration file
@@ -649,7 +656,7 @@ if ($status_bin == 0  && $status_pdfjam == 0 &&  !(-e "install_true")) {
                     &mysystem("cp $bashrc $bashrc.copy");
 
 
-                    $i += 1;
+#                    $i += 1;
 
 		    print "\n2) Run this command to remove rp_bin permanantly from the search path.\n";
                     print "\n\tmv $bashrc.minus_rpbin.txt $bashrc\n\n";