README.test → debian/README.test

-otes on how this package can be tested.
+Notes on how this package can be tested.
 
 
 This package can be tested by executing
@@ -7,6 +7,6 @@ This package can be tested by executing
 
 in order to confirm its integrity.
 
-Notes : the sample data are recovered from; https://github.com/arq5x/  They are both ‘.BED’ 
+Note: The sample data are recovered from https://github.com/arq5x/  They are both ‘.BED’ 
 file extensions. However the macs package install instructions is
 using the ‘BAM’ extension format. If anyone has any recommendation on where to find sample data in this format it will be much appreciated :)

debian/changelog

@@ -3,6 +3,11 @@ macs (2.1.1.20160309-2) UNRELEASED; urgency=medium
   * debian/upstream/metadata:
      - UTF-8 notation of names rather than TeX syntax
      - added eprint
+  * d/rules: Do not parse d/changelog
+  * Remove Tim Booth and H. Soon Gweon from Uploaders
+  * Standards-Version: 4.1.3
+  * hardening=+all
+  * debhelper 11
 
  -- Andreas Tille <tille@debian.org>  Wed, 10 Aug 2016 08:15:22 +0200
 

debian/compat

-9
+11

debian/control

 Source: macs
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
-           Tim Booth <tbooth@ceh.ac.uk>,
-           H. Soon Gweon <hyugwe@ceh.ac.uk>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all-dev,
                python-numpy,
                python-setuptools,
                help2man,
                cython
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/macs.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/macs.git
 Homepage: http://github.com/taoliu/MACS/

debian/docs

 README.rst
+debian/README.test
+debian/tests/run-unit-test
\ No newline at end of file

debian/macs-example-data.install

-debian/examples/aluY.chr1.bed	usr/share/doc/macs/examples
-debian/examples/gerp.chr1.bed	usr/share/doc/macs/examples
-debian/README.test		usr/share/doc/macs
-debian/tests/run-unit-test	usr/share/doc/macs

debian/macs.examples

-examples/*
 debian/examples/*
-release/common/*.tree

debian/rules

 #!/usr/bin/make -f
 
 export PYBUILD_NAME=MACS2
-export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
-DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+include /usr/share/dpkg/default.mk
+
 subcommands=callpeak bdgpeakcall bdgbroadcall bdgcmp bdgopt cmbreps bdgdiff \
 	      filterdup predictd pileup randsample refinepeak
 tagline=\- Model\-based Analysis for ChIP\-Sequencing
@@ -26,7 +27,7 @@ override_dh_auto_build:
 		> debian/macs2_$${subcommand}-man-include; done
 	for subcommand in ${subcommands}; do \
 		PYTHONPATH=./.pybuild/pythonX.Y_2.7/build/ help2man \
-		--no-discard-stderr --no-info --version-string="$(VERSION)" \
+		--no-discard-stderr --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \
 		--include debian/macs2_$${subcommand}-man-include \
 		"python bin/macs2 $${subcommand}" > \
 		debian/macs2_$${subcommand}.1; done

debian/tests/run-unit-test

@@ -13,6 +13,7 @@ fi
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
+gunzip *.gz
 
 macs2 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
 macs2 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1