debian/changelog

-kraken (1.1-3) UNRELEASED; urgency=medium
+kraken (1.1-3) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Trim trailing whitespace.
   * Use secure copyright file specification URI.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Wed, 24 Oct 2018 21:58:35 +0000
+  [ Andreas Tille ]
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.3.0
+  * Fix Perl interpreter path
+  * propagate build options
+
+ -- Andreas Tille <tille@debian.org>  Mon, 07 Jan 2019 13:15:32 +0100
 
 kraken (1.1-2) unstable; urgency=medium
 

debian/control

@@ -5,9 +5,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                jellyfish1
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kraken.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/kraken.git
+Standards-Version: 4.3.0
+Vcs-Browser: https://salsa.debian.org/med-team/kraken
+Vcs-Git: https://salsa.debian.org/med-team/kraken.git
 Homepage: http://ccb.jhu.edu/software/kraken/
 
 Package: kraken

debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 07 Jan 2019 13:14:41 +0100
+Description: propagate build options
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,5 +1,5 @@
+ CXX = g++
+-CXXFLAGS = -Wall -fopenmp -O3
++CXXFLAGS += -Wall -fopenmp -O3
+ PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator
+ 
+ .PHONY: all install clean

debian/patches/series

 use_jellyfish1.patch
 kraken_tmp_dir.patch
 fix_reading_fasta.patch
+hardening.patch

debian/rules

@@ -20,3 +20,9 @@ override_dh_link:
 override_dh_auto_install:
 	dh_auto_install -- KRAKEN_DIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)
 	./install_kraken.sh /usr/lib/$(DEB_SOURCE) $(DEB_SOURCE)
+
+override_dh_install:
+	dh_install
+	for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done