debian/changelog

+hisat2 (2.1.0-2) unstable; urgency=medium
+
+  * Team upload.
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Fix wrong path for Perl interpreter
+  * Do not parse d/changelog
+
+ -- Andreas Tille <tille@debian.org>  Mon, 24 Sep 2018 11:52:06 +0200
+
 hisat2 (2.1.0-1) unstable; urgency=medium
 
   * Team upload

debian/compat

-10
+11

debian/control

 Source: hisat2
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
-Build-Depends: debhelper (>= 10),
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
                help2man,
                pandoc,
                python
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/hisat2.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/hisat2.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/hisat2
+Vcs-Git: https://salsa.debian.org/med-team/hisat2.git
 Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml
 
 Package: hisat2
 Architecture: amd64 kfreebsd-amd64
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, python
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${perl:Depends},
+         python
 Description: graph-based alignment of short nucleotide reads to many genomes
  HISAT2 is a fast and sensitive alignment program for mapping next-generation
  sequencing reads (both DNA and RNA) to a population of human genomes (as well

debian/rules

@@ -7,14 +7,16 @@ export TZ=UTC
 # for hardening you might like to uncomment this:
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
-DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+include /usr/share/dpkg/default.mk
+
+DATE=$(shell date --date=@$(SOURCE_DATE_EPOCH) '+%d %B %Y')
 
 %:
 	dh $@
 
 override_dh_auto_build:
-	make BUILD_HOST='Debian ${DEBFLAVOR}' \
-		BUILD_TIME="$(shell date --date=@`dpkg-parsechangelog --show-field Timestamp`)" \
+	make BUILD_HOST='Debian' \
+		BUILD_TIME="$(DATE)" \
 		all doc
 	help2man ./hisat2 --no-info --name \
 		'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \
@@ -37,3 +39,8 @@ override_dh_auto_build:
 	help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \
 		--no-info > debian/hisat2-inspect-s.1
 
+override_dh_install:
+	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

debian/watch

 version=4
 opts="pasv,repack,compression=xz" \
       ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-([0-9.]+)-source.zip
+
+# Download tarball is very strangely named on Github - this will not work
+# https://github.com/infphilo/hisat2/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
+