debian/changelog

+tophat (2.1.1+dfsg1-3) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #938677
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/control
+  * Set upstream metadata fields: Bug-Submit.
+  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+  * Rely on pre-initialized dpkg-architecture variables.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 11 Oct 2019 09:54:16 +0200
+
 tophat (2.1.1+dfsg1-2) unstable; urgency=medium
 
   * Fix Makefile.am

debian/compat

-11

debian/control

@@ -5,16 +5,16 @@ Uploaders: Carlos Borroto <carlos.borroto@gmail.com>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libbam-dev,
                zlib1g-dev,
-               python,
-               seqan-dev (>= 1.4),
+               python3,
+               seqan-dev,
                libboost-system-dev,
                libboost-thread-dev,
                help2man,
                bowtie
-Standards-Version: 4.2.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/tophat
 Vcs-Git: https://salsa.debian.org/med-team/tophat.git
 Homepage: http://ccb.jhu.edu/software/tophat
@@ -23,7 +23,7 @@ Package: tophat
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python,
+         python3,
          bowtie2 | bowtie,
          samtools (>= 1.5)
 Suggests: cufflinks

debian/patches/series

@@ -4,3 +4,4 @@ fix-gcc6.patch
 remove-convenience-copy-of-samtools.patch
 fix-compatibility-with-recent-samtools.patch
 fix_makefile.am.patch
+2to3.patch

debian/rules

@@ -8,7 +8,7 @@ mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1
 bindir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin
 
 # according to dpkg-architecture(1) this should be set to support manual invocation
-DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+include /usr/share/dpkg/architecture.mk
 
 %:
 	dh $@ --no-parallel

debian/upstream/metadata

-Contact: Cole Trapnell <cole@cs.umd.edu>
-Name: TopHat
 Reference:
   author: Cole Trapnell and Lior Pachter and Steven L. Salzberg
   title: >
@@ -12,8 +10,7 @@ Reference:
   DOI: 10.1093/bioinformatics/btp120
   PMID: 19289445
   URL: http://bioinformatics.oxfordjournals.org/content/25/9/1105.short
-  eprint: "http://bioinformatics.oxfordjournals.org/content/\
-    25/9/1105.full.pdf+html"
+  eprint: "http://bioinformatics.oxfordjournals.org/content/25/9/1105.full.pdf+html"
   license: Open Access
 Registry:
 - Name: OMICtools
@@ -22,3 +19,4 @@ Registry:
   Entry: tophat
 - Name: SciCrunch
   Entry: SCR_013035
+Bug-Submit: tophat.cufflinks@gmail.com