debian/changelog

+samtools-legacy (0.1.19-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Switch from cdbs to dh
+  * Add watch file
+  * Cleanup debian/upstream/metadata
+  * cme fix dpkg-control
+     - Point VCS fields to Salsa
+     - Standards-Version: 4.1.4
+     - Fix spacing in short description
+  * debhelper 11
+  * Fix Homepage
+
+ -- Andreas Tille <tille@debian.org>  Tue, 03 Jul 2018 13:50:54 +0200
+
 samtools-legacy (0.1.19-2) unstable; urgency=medium
 
   1bb181e Build libbam-dev from version 0.1.19 in a “legacy” source package.

debian/clean

+examples/calDepth
+examples/ex1.bam
+examples/ex1.bam.bai
+examples/ex1.fa.fai
+examples/ex1.glf
+examples/ex1.glfview.gz
+examples/ex1.pileup.gz
+examples/ex1a.bam
+examples/ex1b.bam
+examples/ex1f-rmduppe.bam
+examples/ex1f-rmdupse.bam
+examples/ex1f.bam
+examples/ex1f.rg
+examples/ex1.bcf

debian/compat

-9
+11

debian/control

@@ -3,15 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Charles Plessy <plessy@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
-               cdbs,
-               quilt,
+Build-Depends: debhelper (>= 11~),
                libncurses5-dev,
                zlib1g-dev
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git
-Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git -b samtools-legacy
-Homepage: http://samtools.sourceforge.net
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/samtools-legacy
+Vcs-Git: https://salsa.debian.org/med-team/samtools-legacy.git
+Homepage: http://www.htslib.org/
 
 Package: libbam-dev
 Architecture: any

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SAM tools
 Source: https://github.com/samtools/samtools/archive/0.1.19.tar.gz
 
 Files: *

debian/gbp.conf

@@ -6,9 +6,6 @@ debian-branch = debian/samtools-legacy
 upstream-tag = upstream/0.1.19
 pristine-tar = True
 
-# use pristine-tar:
-pristine-tar = True
-
-[git-dch]
+[dch]
 # include 7 digits of the commit id in the changelog enty:
 id-length = 7

debian/rules

 #!/usr/bin/make -f
 
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
-
 CFLAGS += -fPIC $(LDFLAGS) $(CPPFLAGS)
 
-DEB_MAKE_BUILD_TARGET = all all-recur razip lib
-DEB_MAKE_CHECK_TARGET = -C examples all
+%:
+	dh $@
+
+override_dh_auto_build:
+	dh_auto_build -- all all-recur razip lib
 
-clean::
-	$(RM) examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	$(MAKE) -C examples all
+endif

debian/upstream/metadata

-Archive: SourceForge
-Changelog: https://raw.github.com/samtools/samtools/HEAD/NEWS
-Homepage: http://samtools.sourceforge.net
-mr:
-  checkout: debcheckout -a git://git.debian.org/debian-med/samtools.git
-Name: SAM tools
 Reference: 
  author: Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue Ruan and Nils Homer and Gabor Marth and Goncalo Abecasis and Richard Durbin and 1000 Genome Project Data Processing Subgroup
  title: The Sequence Alignment/Map (SAM) Format and SAMtools

debian/watch

+version=4
+
+https://github.com/samtools/samtools/releases?after=0.2.0-rc1 .*/archive/(0\.1\.\d+)\.tar\.gz