debian/changelog

+tophat (2.1.1+dfsg1-2) UNRELEASED; urgency=medium
+
+  * Fix Makefile.am
+    Closes: #906510
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.0
+
+ -- Andreas Tille <tille@debian.org>  Sat, 18 Aug 2018 08:44:34 +0200
+
 tophat (2.1.1+dfsg1-1) unstable; urgency=medium
 
   * Team upload

debian/compat

-10
+11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Carlos Borroto <carlos.borroto@gmail.com>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libbam-dev,
                zlib1g-dev,
                python,
@@ -14,9 +14,9 @@ Build-Depends: debhelper (>= 10),
                libboost-thread-dev,
                help2man,
                bowtie
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/tophat.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/tophat.git
+Standards-Version: 4.2.0
+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
 
 Package: tophat

debian/patches/fix_makefile.am.patch

+Description: Fix Makefile.am
+Bug-Debian: https://bugs.debian.org/906510
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 18 Aug 2018 08:44:34 +0200
+
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -707,31 +707,31 @@ libgc_a_SOURCES = \
+ #-- program sources
+ 
+ prep_reads_SOURCES = prep_reads.cpp
+-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++prep_reads_LDADD = libtophat.a $(BAM_LIB)
+ prep_reads_LDFLAGS = $(LDFLAGS) 
+ 
+ segment_juncs_SOURCES = segment_juncs.cpp
+-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ long_spanning_reads_SOURCES = long_spanning_reads.cpp
+-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ gtf_juncs_SOURCES = gtf_juncs.cpp
+-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ gtf_juncs_LDFLAGS = $(LDFLAGS)
+ 
+ juncs_db_SOURCES = juncs_db.cpp
+-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++juncs_db_LDADD = libtophat.a $(BAM_LIB)
+ juncs_db_LDFLAGS = $(LDFLAGS)
+ 
+ tophat_reports_SOURCES = tophat_reports.cpp
+-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
++tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+ tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS)
+ 
+ fix_map_ordering_SOURCES = fix_map_ordering.cpp
+-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
+ fix_map_ordering_LDFLAGS = $(LDFLAGS)
+ 
+ bam2fastx_SOURCES = bam2fastx.cpp
+@@ -739,18 +739,18 @@ bam2fastx_LDADD = $(top_builddir)/src/li
+ bam2fastx_LDFLAGS = $(LDFLAGS)
+ 
+ bam_merge_SOURCES = bam_merge.cpp
+-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
++bam_merge_LDADD = libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
+ bam_merge_LDFLAGS = $(LDFLAGS)
+ 
+ sam_juncs_SOURCES = sam_juncs.cpp
+-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
++sam_juncs_LDADD = libtophat.a $(BAM_LIB)
+ sam_juncs_LDFLAGS = $(LDFLAGS)
+ 
+ map2gtf_SOURCES = map2gtf.cpp
+-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
+ map2gtf_LDFLAGS = $(LDFLAGS)
+ 
+ gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
+-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
++gtf_to_fasta_LDADD =  libtophat.a libgc.a $(BAM_LIB)
+ gtf_to_fasta_LDFLAGS = $(LDFLAGS)
+ 

debian/patches/series

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