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config entry to make scripts run in serial mode #59

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705eec2
if running in a non-hpc environment it is possible to set serial to …
Dec 20, 2018
969e54c
removed default serial = 0, as the module crashes if the variable is …
Dec 20, 2018
c9284e1
changed the trans function so we dont break old config files
Dec 20, 2018
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15 changes: 10 additions & 5 deletions rp_bin/Ricopili/Utils.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -74,12 +74,17 @@ while (my $line = <FILE>){
}
close FILE;

# return config value, if a default is provided that is returned in case
# the value is not set in the config file
# Otherwise the call resuts in a die call
sub trans {
my ($expr) = @_;
unless (exists $conf{$expr}) {
die "config file without entry: $expr\n";
}
$conf{$expr};
my ($expr, $default) = @_;

return $conf{ $expr} if (exists $conf{$expr});

return $default if ( defined $default );

die "config file without entry: $expr\n";
}


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3 changes: 2 additions & 1 deletion rp_bin/clump_nav3
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Expand Up @@ -23,6 +23,7 @@ my $qloc = &trans("queue");
#my $hmloc = &trans("hmloc");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $serial = &trans("serial", 0);


#######################################
Expand Down Expand Up @@ -102,7 +103,7 @@ GetOptions( "outname=s"=> \$outname,
"det=i"=> \$detformat,

"force1"=> \my $force1,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,

"noclean"=> \my $noclean,
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3 changes: 2 additions & 1 deletion rp_bin/impute_dirsub
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Expand Up @@ -155,6 +155,7 @@ my $i2loc = &trans("i2loc");
my $liloc = &trans("liloc");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $serial = &trans("serial", 0);


###############################################
Expand Down Expand Up @@ -511,7 +512,7 @@ GetOptions(
"triset=s"=> \my $trioset_file,

"help"=> \my $help,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,

"sleep=i"=> \my $sleep_sw,
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3 changes: 2 additions & 1 deletion rp_bin/pcaer
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Expand Up @@ -23,6 +23,7 @@ my $qloc = &trans("queue");
my $hmloc = &trans("hmloc");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $serial = &trans("serial", 0);

#######################################
## v12: with pops as reference
Expand Down Expand Up @@ -168,7 +169,7 @@ my $sepa = 1;
use Getopt::Long;
GetOptions( "out=s"=> \$outname,
"help"=> \my $help,
"serial"=> \my $serial,
"serial"=> $serial,
"sleep=i"=> \my $sleep_sw,

"trio"=> \my $trio,
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3 changes: 2 additions & 1 deletion rp_bin/postimp_navi
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Expand Up @@ -174,6 +174,7 @@ my $qloc = &trans("queue");
my $i2loc = &trans("i2loc");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $serial = &trans("serial", 0);


#exit;
Expand Down Expand Up @@ -359,7 +360,7 @@ GetOptions(
"allsw"=> \my $allsw,
"cox"=> \my $cox,
"outname=s"=> \my $outname,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,

"sleep=i"=> \my $sleep_sw,
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3 changes: 2 additions & 1 deletion rp_bin/preimp_dir
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Expand Up @@ -38,6 +38,7 @@ my $qloc = &trans("queue");
my $init = &trans("init");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $serial = &trans("serial", 0);


my $mind=0.02; # per ID
Expand Down Expand Up @@ -133,7 +134,7 @@ use Getopt::Long;
GetOptions(

"trio"=> \my $trio,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,

"sleep=i"=> \my $sleep_sw,
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3 changes: 2 additions & 1 deletion rp_bin/refdir_navi
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Expand Up @@ -99,6 +99,7 @@ my $hmloc = &trans("hmloc");
my $email = &trans("email");
my $loloc = &trans("loloc");
my $bcrloc = &trans("bcrloc");
my $serial = &trans("serial", 0);

#######################################

Expand Down Expand Up @@ -186,7 +187,7 @@ GetOptions(
"qheadd=i"=> \$q16_head,
"mac_th=i"=> \$mac_th,
"walltimeplus=i"=> \$walltimeplus,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,

);
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1 change: 1 addition & 0 deletions rp_bin/rp_config
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Expand Up @@ -119,6 +119,7 @@ rp_logfiles
---- jobarray and queueing parameters:
----------------------------------------
----------------------------------------
serial 0
batch_jobcommand
batch_memory_request
batch_walltime
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4 changes: 2 additions & 2 deletions rp_bin/rp_test_navi
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Expand Up @@ -28,10 +28,10 @@ print "$rp_header\n";
my $loloc = &trans("loloc");
my $email = &trans("email");
my $force1 = 0;
my $serial = 0;
my $outname = "test";
my $job_bn_th = 1000;
my $sepa = 1;
my $serial = &trans("serial", 0);


#######################################
Expand All @@ -51,7 +51,7 @@ my $walltime = 4;
use Getopt::Long;
GetOptions(
"help"=> \my $help,
"serial"=> \my $serial,
"serial"=> $serial,
"sepa=i"=> \$sepa,
"noldsc"=> \my $noldsc,

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4 changes: 2 additions & 2 deletions rp_bin/tarse_navi2
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Expand Up @@ -29,7 +29,7 @@ my $qloc = &trans("queue");
my $hmloc = &trans("hmloc");
my $loloc = &trans("loloc");
my $email = &trans("email");

my $serial = &trans("serial", 0);



Expand Down Expand Up @@ -65,7 +65,7 @@ GetOptions(
"target=s"=> \$target,
"password=s"=> \$password,

"serial"=> \my $serial,
"serial"=> $serial,
"force1"=> \my $force1,
"sjamem_incr=i"=> \$sjamem_incr,
"outname=s"=> \my $outname,
Expand Down