debian/changelog

+centrifuge (1.0.3~beta-2) unstable; urgency=medium
+
+  * Move hisat2 and jellyfish to Build-Depends to make sure package builds
+    only on those architectures where it can be installed later
+  * -msse2 is already enabled by default on amd64 (which is the only
+    architecture the package runs anyway)
+    Closes: #890378
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Wed, 14 Feb 2018 14:18:27 +0100
+
 centrifuge (1.0.3~beta-1) unstable; urgency=low
 
   * Initial release (Closes: #886463)

debian/compat

-10
+11

debian/control

@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 11~),
+               hisat2,
+               jellyfish
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/centrifuge.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/centrifuge.git

debian/patches/no_msse2.patch

+Description: -msse2 is already enabled by default on amd64 (which is the only 
+    architecture the package runs anyway)
+Bug-Debian: https://bugs.debian.org/890378
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 14 Feb 2018 14:12:11 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -160,7 +160,7 @@ endif
+ ifeq (64,$(BITS))
+ 	BITS_FLAG = -m64
+ endif
+-SSE_FLAG=-msse2
++SSE_FLAG=
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""

debian/patches/series

@@ -2,3 +2,4 @@ fix_auto_ptr_usage_in_gcc-7.patch
 0002-Fix-build-with-rank.patch
 0003-Fix-make-install-DESTDIR.patch
 hardening.patch
+no_msse2.patch