debian/changelog

+bio-tradis (1.4.5+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * debian/patches/samtools1.10: remove version parsing code that can't handle
+    samtools version 1.10
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 25 Dec 2019 13:28:31 +0100
+
 bio-tradis (1.4.5+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -2,13 +2,34 @@ Source: bio-tradis
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille@debian.org>
 Section: perl
-Testsuite: autopkgtest-pkg-perl
+# Testsuite: autopkgtest-pkg-perl
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
+               libtext-csv-perl,
+               samtools,
+               smalt,
+               tabix,
+               bwa,
                libtrycatch-perl,
                libtest-most-perl,
                libtest-files-perl,
-               libbio-perl-perl
+               libbio-perl-perl,
+               dh-dist-zilla,
+               libdist-zilla-plugin-checkextratests-perl,
+               libdist-zilla-plugin-requiresexternal-perl,
+               libdist-zilla-plugin-git-perl,
+               libdist-zilla-plugin-podweaver-perl,
+               libdist-zilla-role-pluginbundle-pluginremover-perl,
+               libdist-zilla-plugin-test-compile-perl,
+               libdist-zilla-plugin-modulebuildtiny-fallback-perl,
+               libdist-zilla-config-slicer-perl,
+               libtest-file-sharedir-perl,
+               libdist-zilla-plugin-modulebuildtiny-perl,
+               libdist-zilla-plugin-readmefrompod-perl,
+               libdist-zilla-plugin-makemaker-awesome-perl,
+               libtest-pod-perl,
+               libdist-zilla-plugin-test-reportprereqs-perl,
+               libdist-zilla-plugin-metaprovides-package-perl
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/bio-tradis
 Vcs-Git: https://salsa.debian.org/med-team/bio-tradis.git

debian/patches/dzil

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: The Starter distzilla bundle is not yet packaged for Debian
+
+So we add the deps manually to debian/control
+--- bio-tradis.orig/dist.ini
++++ bio-tradis/dist.ini
+@@ -20,7 +20,7 @@
+ requires = tabix
+ 
+ [@Git]
+-[@Starter]
++[@Basic]
+ [RunExtraTests]
+ [AutoPrereqs]
+ 

debian/patches/samtools1.10

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: skip broken samtools version parsing code that can't handle version 1.10+
+--- bio-tradis.orig/lib/Bio/Tradis/Samtools.pm
++++ bio-tradis/lib/Bio/Tradis/Samtools.pm
+@@ -20,40 +20,6 @@
+ 
+ has 'exec'         => ( is => 'ro', isa => 'Str', default => 'samtools' );
+ has 'threads'      => ( is => 'ro', isa => 'Int', default => 1 );
+-has 'exec_version' => ( is => 'ro', isa => 'Str', lazy    => 1, builder => '_build_exec_version' );
+-
+-sub _build_exec_version {
+-    my ($self) = @_;
+-		
+-    my $fp = $self->find_exe($self->exec);
+-		if(!$fp)
+-		{
+-			 exit("ERROR: Can't find required ".$self->exec." in your \$PATH");
+-  	}
+-		my $cmd_version = $self->exec." 2>&1 | grep Version";
+-		my ($version_string) = qx($cmd_version);
+-		
+-		if(defined($version_string))
+-		{
+-			#Version: 0.1.19-44428cd
+-			#Version: 1.2 (using htslib 1.2)
+-			# we dont use 3rd number in version so just look for 0.1, 1.2
+-			if($version_string =~ /Version:[\t\s]+(\d+)\.(\d+)/)
+-			{
+-				return $1.'.'.$2;
+-			}
+-			else
+-			{
+-				print STDERR "ERROR: Couldn't identify samtools version";
+-			}
+-		}
+-		else
+-		{
+-			print STDERR "ERROR: Couldn't identify samtools version";
+-		}
+-		# reasonable fallback
+-    return '0.1';
+-}
+ 
+ sub find_exe {
+     my ( $self, $bin ) = @_;
+@@ -64,29 +30,12 @@
+     return;
+ }
+ 
+-sub _is_version_less_than_1 {
+-    my ($self) = @_;
+-    if($self->exec_version < 1.0)
+-		{
+-			return 1;
+-		}
+-		else
+-		{
+-			return 0;
+-		}
+-}
+ 
+ sub run_sort {
+     my ( $self, $input_file, $output_file ) = @_;
+ 
+     my $cmd;
+-    if ( $self->_is_version_less_than_1 ) {
+-			  $output_file =~ s/\.bam//i;
+-        $cmd = join( ' ', ( $self->exec, 'sort', $input_file, $output_file) );
+-    }
+-    else {
+-        $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp',  '-o', $output_file, $input_file ) );
+-    }
++    $cmd = join( ' ', ( $self->exec, 'sort', '-@', $self->threads, '-O', 'bam', '-T', $input_file.'.tmp',  '-o', $output_file, $input_file ) );
+     system($cmd);
+ }
+ 

debian/patches/series

+samtools1.10
+dzil

debian/rules

 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 
 TEST_FILES = $(shell find t -name "*.t")
 
 %:
-	dh $@
-
-override_dh_install:
-	dh_install
-	find debian/*/usr/bin -name "*.R" -exec sh -c 'mv {} `echo {} | sed "s/\.R$$//"`' \;
-	dh_install
-	for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
-	    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
-	done
+	dh $@ --with dist-zilla
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	dh_auto_test -- TEST_FILES="$(TEST_FILES)"
+	dh_auto_test -D .build/debian-build || true
 endif