debian/changelog

 blasr (5.3.2-1) UNRELEASED; urgency=medium
 
+  * Team upload
+
   [ Andreas Tille ]
   * New upstream version
   * Build-Depends: libpbdata-dev
     Closes: #906811
   * d/watch: point to Github since upstream is now tagging releases
   * Point Vcs fields to salsa.debian.org
-  * Standards-Version: 4.2.0
+  * debhelper 12
+  * Standards-Version: 4.3.0
   * Build system switched from cmake to meson
-  TODO:
-    meson.build:57:0: ERROR:  Native dependency 'libblasr' not found
-    --> https://salsa.debian.org/med-team/libblasr
+  * Versioned Build-Depends: libblasr-dev
+  * Cleanup d/rules
 
   [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.

debian/compat

-11
+12

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                python,
                meson,
                pkg-config,
@@ -13,8 +13,9 @@ Build-Depends: debhelper (>= 11~),
                libpbseq-dev (>= 0~20160912),
                libpbbam-dev (>= 0.18.0~),
                libpbdata-dev,
-               libgtest-dev
-Standards-Version: 4.2.0
+               libgtest-dev,
+               libblasr-dev (>= 5.3.1+dfsg-2)
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/blasr
 Vcs-Git: https://salsa.debian.org/med-team/blasr.git
 Homepage: https://github.com/PacificBiosciences/blasr

debian/docs

-README.md
-README.MANUAL.md
+README*

debian/install

-blasr	usr/bin
-utils/loadPulses	usr/bin
-utils/pls2fasta		usr/bin
-utils/samtoh5		usr/bin
-utils/samtom4		usr/bin
-utils/samFilter		usr/bin
-utils/toAfg		usr/bin
-utils/sawriter		usr/bin
-utils/sdpMatcher	usr/bin
-utils/bax2bam/bin/*	usr/bin
-utils/bam2bax/bin/*	usr/bin
+# Does not belong to default build any more
+#utils/loadPulses	usr/bin
+#utils/pls2fasta		usr/bin
+#utils/samtoh5		usr/bin
+#utils/samtom4		usr/bin
+#utils/samFilter		usr/bin
+#utils/toAfg		usr/bin
+#utils/sawriter		usr/bin
+#utils/sdpMatcher	usr/bin
+#utils/bax2bam/bin/*	usr/bin
+#utils/bam2bax/bin/*	usr/bin

debian/patches/use_debian_packaged_pblibs.patch

 --- a/meson.build
 +++ b/meson.build
-@@ -51,10 +51,10 @@ blasr_thread_dep = dependency('threads',
+@@ -51,15 +51,19 @@ blasr_thread_dep = dependency('threads',
  blasr_boost_dep = dependency('boost', required : true)
  
  # pbbam
@@ -13,3 +13,23 @@
  
  # zlib
  blasr_zlib_dep = dependency('zlib', required : true)
+ 
+-blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep]
++# missing libs for linker
++samwriter_pbdata_deps = cpp.find_library('pbdata')
++blasr_pbihdf_deps = cpp.find_library('pbihdf')
++
++blasr_deps = [blasr_thread_dep, blasr_boost_dep, blasr_pbbam_dep, blasr_libblasr_dep, blasr_zlib_dep, samwriter_pbdata_deps, blasr_pbihdf_deps]
+ 
+ ########################
+ # sources + executable #
+@@ -110,7 +114,8 @@ blasr_main = executable(
+   install : true,
+   dependencies : blasr_deps,
+   link_with : blasr_static_impl,
+-  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'])
++  cpp_args : [blasr_warning_flags, '-DUSE_PBBAM=1', '-DCMAKE_BUILD=1'],
++)
+ 
+ blasr_utils_sawriter = executable(
+   'sawriter', files([

debian/rules

@@ -33,27 +33,21 @@ export DEB_CXXFLAGS_MAINT_PREPEND = $(CPPFLAGS) -I$(PBDATA_ROOT_DIR)
 	dh $@ --buildsystem=meson
 
 override_dh_auto_configure:
-#	./configure.py --shared
-	LDFLAGS="-L$(HTSLIB_LIB) -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem $(HDF5_INC)" meson -Dtests=false build .
+	LDFLAGS="-L$(HTSLIB_LIB) -L$(HDF5_LIB) -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem $(HDF5_INC)" meson -Dtests=false -Dprefix=/usr build .
 
-#override_dh_auto_build: main bax2bam bam2bax;
-
-.PHONY: bax2bam
 bax2bam: utils/bax2bax/bin/bax2bam
 utils/bax2bax/bin/bax2bam:
 	$(MAKE) -C utils/bax2bam
 
-.PHONY: bam2bax
 bam2bax: utils/bam2bax/bin/bam2bax
 utils/bam2bax/bin/bam2bax:
 	$(MAKE) -C utils/bam2bax
 
-# Tests require data not available in the source distribution
-override_dh_auto_test: ;
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+override_dh_auto_test:
+	echo Tests require data not available in the source distribution
+endif
 
-#override_dh_auto_clean: override_dh_auto_configure
-#	$(MAKE) clean
-#	$(MAKE) -C utils/bam2bax clean
-#	$(MAKE) -C utils/bax2bam clean
-#	# This is created by configure.py
-#	$(RM) defines.mk
+override_dh_auto_build:
+	ln -s build obj-$(DEB_BUILD_GNU_TYPE)
+	dh_auto_build