diff --git a/rp_bin/Ricopili/Version.pm b/rp_bin/Ricopili/Version.pm index 20e7246..6dc3eb9 100644 --- a/rp_bin/Ricopili/Version.pm +++ b/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 $rp_logo = <<'END_TXT'; diff --git a/rp_bin/blueprint b/rp_bin/blueprint index 7b521d8..0f87363 100755 --- a/rp_bin/blueprint +++ b/rp_bin/blueprint @@ -59,6 +59,11 @@ if ($qloc eq "custom") { $batch_ncores_per_node = &trans("batch_ncores_per_node"); $batch_mem_per_node = &trans("batch_mem_per_node"); } +else { + print "Error: pipeline only runs in custom mode meanwhile\n"; + print " please reinstall\n"; + exit; +} diff --git a/rp_bin/my.prepvcf_filtnorm b/rp_bin/my.prepvcf_filtnorm index c4ba98e..f35ca38 100755 --- a/rp_bin/my.prepvcf_filtnorm +++ b/rp_bin/my.prepvcf_filtnorm @@ -104,6 +104,11 @@ if ($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"; diff --git a/rp_bin/my.start_job b/rp_bin/my.start_job index f8c7949..beb4a3f 100755 --- a/rp_bin/my.start_job +++ b/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) diff --git a/rp_bin/refdir_navi b/rp_bin/refdir_navi index 62426e5..8d1b7bf 100755 --- a/rp_bin/refdir_navi +++ b/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){ diff --git a/rp_bin/rp_config b/rp_bin/rp_config index 6068639..ba80af3 100755 --- a/rp_bin/rp_config +++ b/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";