debian/README.Debian

@@ -65,7 +65,7 @@ From: Scott Christley <schristley@mac.com>:
   From looking at the bowtie output you provided, the content is the same.
   The sequence id names, position and mismatches are identical in both
   outputs, the only difference is the order.  That may not even be
-  bowtie's fault, it may be using some system or other library which
+  bowtie's fault, it may be using some systems or other library which
   does sorting slightly differently, and most specifically handling ties
   differently.
 

debian/changelog

+bowtie (1.2.2+dfsg-3) unstable; urgency=medium
+
+  * Fix watch file to not detect beta versions
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Wed, 23 May 2018 17:59:29 +0200
+
 bowtie (1.2.2+dfsg-2) unstable; urgency=medium
 
   * Update d/tests/run-unit-test

debian/control

@@ -13,9 +13,9 @@ Build-Depends: debhelper (>= 11),
                python,
                seqan-dev (>= 1.4),
                zlib1g-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bowtie.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bowtie.git
+Standards-Version: 4.1.4
+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/
 
 Package: bowtie

debian/patches/gcc-64bit.patch

@@ -6,7 +6,7 @@ Description: Use gcc to determine if an arch is 64-bit
    on x86_64). This is common on the mips buildds.
  Therefore ask GCC if this architecture is 64-bit. Using __LP64__ is the easiest
  method, but is not portable and probably only works with GCC and Clang
- unfortunatly.
+ unfortunately.
 Author: James Cowgill <jcowgill@debian.org>
 ---
 This patch header follows DEP-3: http://dep.debian.net/deps/dep3/

debian/watch

 version=4
 
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
-  https://github.com/BenLangmead/bowtie/releases .*/archive/v@ANY_VERSION@@ARCHIVE_EXT@
+  https://github.com/BenLangmead/bowtie/releases .*/archive/v(\d[-.\d]+)@ARCHIVE_EXT@