debian/changelog

-rsem (1.3.0+dfsg-1) UNRELEASED; urgency=medium
+rsem (1.3.0+dfsg-1) experimental; urgency=medium
 
   * New upstream version
   * d/watch:
      - version=4
      - xz compression
   * remove code copy of samtools-1.3
+  * cme fix dpkg-control
+  * debhelper 11
+  * d/rules: do not parse d/changelog
 
- -- Andreas Tille <tille@debian.org>  Fri, 09 Dec 2016 14:26:08 +0100
+ -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 20:34:37 +0100
 
 rsem (1.2.31+dfsg-1) unstable; urgency=medium
 

debian/compat

-9
+11

debian/control

@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
            Andreas Tille <tille@debian.org>
 Section: science
-Priority: extra
-Build-Depends: debhelper (>= 9),
+Priority: optional
+Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                libncurses5-dev,
                libboost-dev,
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 9),
 # bowtie is a run-time dependency available on only a few systems, not actually
 # needed for building but it prevents the creation of uninstallable packages
                bowtie | bowtie2
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git
 Homepage: http://deweylab.biostat.wisc.edu/rsem/

debian/copyright

@@ -30,45 +30,6 @@ License: GPL-3
  On Debian systems, the full text of the GNU General Public
  License version 3 can be found in the file
  `/usr/share/common-licenses/GPL-3'.
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz
-
-Files: samtools-1.3/*
-Copyright: © 2008–2016, Genome Research Ltd. (GRL)
-           © 2003–2006, 2008–2011, by Heng Li <lh3lh3@live.co.uk>
-           © 2009–2012 Broad Institute
-           © 2010 Illumina, Inc.
-           © 2012–2013 Peter Cock, The James Hutton Institute.
-License: MIT
-Comment: Modified version of samtools included as per upstream
-
-Files: samtools-1.3/win32/xcurses.h
-Copyright: Public Domain
-License: public-domain
- This file is part of PDCurses (http://pdcurses.sourceforge.net/),
- which is in the public domain.
-
-Files: samtools-1.3/win32/z*.h
-Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
-License: zlib
- This software is provided 'as-is', without any express or implied
- warranty.  In no event will the authors be held liable for any damages
- arising from the use of this software.
- .
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
- .
-  1. The origin of this software must not be misrepresented; you must not
-     claim that you wrote the original software. If you use this software
-     in a product, an acknowledgment in the product documentation would be
-     appreciated but is not required.
-  2. Altered source versions must be plainly marked as such, and must not be
-     misrepresented as being the original software.
-  3. This notice may not be removed or altered from any source distribution.
- .
-  Jean-loup Gailly        Mark Adler
-  jloup@gzip.org          madler@alumni.caltech.edu
 
 License: MIT
  Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -88,4 +49,3 @@ License: MIT
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
-

debian/patches/use_debian_packaged_samtools.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 09 Dec 2016 14:26:08 +0100
+Description: Use Debian packaged samtools
+
 --- a/Makefile
 +++ b/Makefile
 @@ -12,7 +12,7 @@ BOOST = .

debian/rules

@@ -2,13 +2,12 @@
 
 DH_VERBOSE := 1
 
-DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+include /usr/share/dpkg/default.mk
 
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@ --parallel
+	dh $@
 
 override_dh_auto_build:
 	dh_auto_build -- BOOST=/usr/include prefix=debian/tmp
@@ -16,13 +15,13 @@ override_dh_auto_build:
 		rsem-control-fdr rsem-generate-ngvector \
 		rsem-plot-transcript-wiggles rsem-prepare-reference \
 		rsem-run-ebseq; do pod2man $${prog} debian/$${prog}.1; done
-	help2man ./rsem-gff3-to-gtf --no-info --version-string="${VERSION}" \
+	help2man ./rsem-gff3-to-gtf --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
 		--name 'Convert GFF3 files to GTF files.' > \
 		debian/rsem-gff3-to-gtf.1
-	help2man ./rsem-bam2wig --no-info --version-string="${VERSION}" \
+	help2man ./rsem-bam2wig --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
 		--name 'Convert BAM files to wiggle files.' > \
 		debian/rsem-bam2wig.1
-	help2man ./rsem-simulate-reads --no-info --version-string="${VERSION}" \
+	help2man ./rsem-simulate-reads --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
 		--name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \
 		debian/rsem-simulate-reads.1