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iap-fix-deprecated-perl-functions.patch
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diff -crB IAP-2.6.1/IAP/annotateVariants.pm IAP-2.6.1-roelj/IAP/annotateVariants.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/annotateVariants.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/annotateVariants.pm 2018-06-27 13:09:54.530481836 +0200
***************
*** 13,20 ****
package IAP::annotateVariants;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runAnnotateVariants {
--- 13,21 ----
package IAP::annotateVariants;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runAnnotateVariants {
***************
*** 153,159 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 154,160 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/baf.pm IAP-2.6.1-roelj/IAP/baf.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/baf.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/baf.pm 2018-06-27 13:08:24.463766554 +0200
***************
*** 10,17 ****
package IAP::baf;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runBAF {
--- 10,17 ----
package IAP::baf;
use strict;
! use File::Temp;
! use File::Basename;
use IAP::sge;
sub runBAF {
***************
*** 168,174 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 168,174 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/baseRecal.pm IAP-2.6.1-roelj/IAP/baseRecal.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/baseRecal.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/baseRecal.pm 2018-06-27 13:09:37.474157052 +0200
***************
*** 10,17 ****
package IAP::baseRecal;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runBaseRecalibration {
--- 10,18 ----
package IAP::baseRecal;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runBaseRecalibration {
***************
*** 144,151 ****
############
sub get_job_id {
! my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 145,152 ----
############
sub get_job_id {
! my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/callableLoci.pm IAP-2.6.1-roelj/IAP/callableLoci.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/callableLoci.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/callableLoci.pm 2018-06-27 13:10:07.697732552 +0200
***************
*** 10,17 ****
package IAP::callableLoci;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runCallableLoci {
--- 10,18 ----
package IAP::callableLoci;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runCallableLoci {
***************
*** 109,115 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 110,116 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/calling.pm IAP-2.6.1-roelj/IAP/calling.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/calling.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/calling.pm 2018-06-27 13:10:40.691360728 +0200
***************
*** 13,20 ****
package IAP::calling;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runVariantCalling {
--- 13,21 ----
package IAP::calling;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runVariantCalling {
***************
*** 236,242 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 237,243 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/check.pm IAP-2.6.1-roelj/IAP/check.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/check.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/check.pm 2018-06-27 13:10:17.009909857 +0200
***************
*** 10,18 ****
package IAP::check;
use strict;
! use POSIX qw(tmpnam);
use FindBin;
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runCheck {
--- 10,19 ----
package IAP::check;
use strict;
! use File::Temp;
! use File::Basename;
use FindBin;
!
use IAP::sge;
sub runCheck {
***************
*** 366,372 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 367,373 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/copyNumber.pm IAP-2.6.1-roelj/IAP/copyNumber.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/copyNumber.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/copyNumber.pm 2018-06-27 13:11:07.875878251 +0200
***************
*** 12,20 ****
package IAP::copyNumber;
use strict;
! use POSIX qw(tmpnam);
use File::Path qw(make_path);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runCopyNumberTools {
--- 12,21 ----
package IAP::copyNumber;
use strict;
! use File::Temp;
! use File::Basename;
use File::Path qw(make_path);
!
use IAP::sge;
sub runCopyNumberTools {
***************
*** 436,442 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 437,443 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/filterVariants.pm IAP-2.6.1-roelj/IAP/filterVariants.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/filterVariants.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/filterVariants.pm 2018-06-27 13:10:47.717494492 +0200
***************
*** 11,18 ****
package IAP::filterVariants;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runFilterVariants {
--- 11,19 ----
package IAP::filterVariants;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runFilterVariants {
***************
*** 149,155 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 150,156 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/mapping.pm IAP-2.6.1-roelj/IAP/mapping.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/mapping.pm 2018-06-27 13:00:14.374417399 +0200
--- b/lib/perl5/site_perl/5.26.1/IAP/mapping.pm 2018-06-27 13:08:31.279896386 +0200
***************
*** 13,20 ****
package IAP::mapping;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runMapping {
--- 13,21 ----
package IAP::mapping;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runMapping {
***************
*** 549,555 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 550,556 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/nipt.pm IAP-2.6.1-roelj/IAP/nipt.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/nipt.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/nipt.pm 2018-06-27 13:11:20.452117655 +0200
***************
*** 11,19 ****
package IAP::nipt;
use strict;
! use POSIX qw(tmpnam);
use FindBin;
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
--- 11,20 ----
package IAP::nipt;
use strict;
! use File::Temp;
! use File::Basename;
use FindBin;
!
use IAP::sge;
***************
*** 82,89 ****
############
sub get_job_id {
! my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
--- 83,90 ----
############
sub get_job_id {
! my $id = tmpnam();
! $id=basename($id);
return $id;
}
diff -crB IAP-2.6.1/IAP/poststats.pm IAP-2.6.1-roelj/IAP/poststats.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/poststats.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/poststats.pm 2018-06-27 13:11:43.980565524 +0200
***************
*** 11,17 ****
package IAP::poststats;
use strict;
! use POSIX qw(tmpnam);
use FindBin;
use IAP::sge;
--- 11,18 ----
package IAP::poststats;
use strict;
! use File::Temp;
! use File::Basename;
use FindBin;
use IAP::sge;
***************
*** 120,127 ****
############
sub get_job_id {
! my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
--- 121,128 ----
############
sub get_job_id {
! my $id = tmpnam();
! $id=basename($id);
return $id;
}
diff -crB IAP-2.6.1/IAP/prestats.pm IAP-2.6.1-roelj/IAP/prestats.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/prestats.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/prestats.pm 2018-06-27 13:08:20.295687159 +0200
***************
*** 10,17 ****
package IAP::prestats;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runPreStats {
--- 10,17 ----
package IAP::prestats;
use strict;
! use File::Temp;
! use File::Basename;
use IAP::sge;
sub runPreStats {
***************
*** 60,66 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 60,66 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/realign.pm IAP-2.6.1-roelj/IAP/realign.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/realign.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/realign.pm 2018-06-27 13:11:31.540328726 +0200
***************
*** 11,18 ****
package IAP::realign;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runRealignment {
--- 11,19 ----
package IAP::realign;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
sub runRealignment {
***************
*** 261,268 ****
############
sub get_job_id {
! my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 262,269 ----
############
sub get_job_id {
! my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/somaticVariants.pm IAP-2.6.1-roelj/IAP/somaticVariants.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/somaticVariants.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/somaticVariants.pm 2018-06-27 13:10:29.514147930 +0200
***************
*** 12,20 ****
package IAP::somaticVariants;
use strict;
! use POSIX qw(tmpnam);
use File::Path qw(make_path);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
### Run and merge
--- 12,21 ----
package IAP::somaticVariants;
use strict;
! use File::Temp;
! use File::Basename;
use File::Path qw(make_path);
!
use IAP::sge;
### Run and merge
***************
*** 729,735 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
--- 730,736 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
diff -crB IAP-2.6.1/IAP/structuralVariants.pm IAP-2.6.1-roelj/IAP/structuralVariants.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/structuralVariants.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/structuralVariants.pm 2018-06-27 13:11:59.171854676 +0200
***************
*** 10,18 ****
package IAP::structuralVariants;
use strict;
! use POSIX qw(tmpnam);
use File::Path qw(make_path);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
sub runStructuralVariantCallers {
--- 10,19 ----
package IAP::structuralVariants;
use strict;
! use File::Temp;
! use File::Basename;
use File::Path qw(make_path);
!
use IAP::sge;
sub runStructuralVariantCallers {
***************
*** 514,520 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 515,521 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/IAP/vcfutils.pm IAP-2.6.1-roelj/IAP/vcfutils.pm
*** a/lib/perl5/site_perl/5.26.1/IAP/vcfutils.pm 2017-11-01 08:47:08.000000000 +0100
--- b/lib/perl5/site_perl/5.26.1/IAP/vcfutils.pm 2018-06-27 13:10:58.306696084 +0200
***************
*** 14,21 ****
package IAP::vcfutils;
use strict;
! use POSIX qw(tmpnam);
! use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::sge;
--- 14,22 ----
package IAP::vcfutils;
use strict;
! use File::Temp;
! use File::Basename;
!
use IAP::sge;
***************
*** 199,205 ****
############
sub get_job_id {
my $id = tmpnam();
! $id=~s/\/tmp\/file//;
return $id;
}
############
--- 200,206 ----
############
sub get_job_id {
my $id = tmpnam();
! $id=basename($id);
return $id;
}
############
diff -crB IAP-2.6.1/illumina_pipeline.pl IAP-2.6.1-roelj/illumina_pipeline.pl
*** a/bin/illumina_pipeline.pl 2017-11-01 08:47:08.000000000 +0100
--- b/bin/illumina_pipeline.pl 2018-06-27 13:13:12.542251048 +0200
***************
*** 10,25 ****
### Load common perl modules ####
use strict;
! use POSIX qw(tmpnam strftime);
use Getopt::Long;
use FindBin;
use File::Path qw(make_path);
use File::Copy qw(copy);
use Cwd qw( abs_path );
! use File::Basename qw( dirname );
### Load pipeline modules ####
- use lib "$FindBin::Bin"; #locates pipeline directory
use IAP::prestats;
use IAP::mapping;
use IAP::poststats;
--- 10,25 ----
### Load common perl modules ####
use strict;
! use File::Temp;
! use POSIX qw(strftime);
use Getopt::Long;
use FindBin;
use File::Path qw(make_path);
use File::Copy qw(copy);
use Cwd qw( abs_path );
! use File::Basename qw( dirname basename );
### Load pipeline modules ####
use IAP::prestats;
use IAP::mapping;
use IAP::poststats;
diff -crB IAP-2.6.1/scripts/run_SAp42ann_on_vcf.pl IAP-2.6.1-roelj/scripts/run_SAp42ann_on_vcf.pl
*** a/share/iap/scripts/run_SAp42ann_on_vcf.pl 2017-11-01 08:47:08.000000000 +0100
--- b/share/iap/scripts/run_SAp42ann_on_vcf.pl 2018-06-26 17:50:00.626871101 +0200
***************
*** 1,6 ****
#!/usr/bin/perl -w
use strict;
! use POSIX qw(tmpnam);
my $email = "i.nijman\@umcutrecht.nl";
--- 1,6 ----
#!/usr/bin/perl -w
use strict;
! use File::Temp;
my $email = "i.nijman\@umcutrecht.nl";
***************
*** 54,57 ****
return $jid2;
! }
\ No newline at end of file
--- 54,57 ----
return $jid2;
! }