debian/changelog

+bowtie (1.2.2+dfsg-4) unstable; urgency=medium
+
+  [ Andreas Tille ]
+  * spelling
+  * Upload to unstable
+
+  [ Dylan Aïssi ]
+  * Update metadata: Add bio.tools ref
+
+  [ Alexandre Mestiashvili ]
+  * Add patch fixing FTBFS, thanks to ch4rr0 at github.com
+    Closes: #906341
+  * Check for DEB_BUILD_OPTIONS and nocheck
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Wed, 05 Sep 2018 14:34:56 +0000
+
 bowtie (1.2.2+dfsg-3) unstable; urgency=medium
 
   * Fix watch file to not detect beta versions

debian/control

@@ -4,7 +4,7 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>,
            Ognyan Kulev <ogi@debian.org>,
            Stephan Struckmann <stephan.struckmann@gmail.com>,
-           Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
+           Alexandre Mestiashvili <mestia@debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11),
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11),
                python,
                seqan-dev (>= 1.4),
                zlib1g-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git
 Homepage: http://bowtie-bio.sourceforge.net/

debian/patches/fix_isa_return.patch

+Subject: Fix isa return type
+From: ch4rr0
+Comment:
+ see https://github.com/BenLangmead/bowtie/commit/58c6ac97b1938909881877ef83167f5eff0e8ab1
+--- bowtie.orig/ebwt.h
++++ bowtie/ebwt.h
+@@ -862,7 +862,7 @@
+ 	TIndexOffU*   ftab() const         { return _ftab; }
+ 	TIndexOffU*   eftab() const        { return _eftab; }
+ 	TIndexOffU*   offs() const         { return _offs; }
+-	uint32_t*   isa() const          { return _isa; } /* check */
++	TIndexOffU*   isa() const          { return _isa; } /* check */
+ 	TIndexOffU*   plen() const         { return _plen; }
+ 	TIndexOffU*   rstarts() const      { return _rstarts; }
+ 	uint8_t*    ebwt() const         { return _ebwt; }

debian/patches/series

+fix_isa_return.patch
 no_hash_style_both_for_mips.patch
 use-dpkg-buildflags.patch
 use_debian_seqan.patch

debian/rules

@@ -44,6 +44,10 @@ override_dh_auto_clean:
 	dh_auto_clean
 
 override_dh_auto_test:
+	# print DEB_BUILD_OPTIONS
+	$(info $$DEB_BUILD_OPTIONS is [${DEB_BUILD_OPTIONS}])
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	ln -s debian/tests
 	sh debian/tests/run-unit-test test_at_build_time
 	rm -f tests examples[0-9].out
+endif