debian/changelog

+trnascan-se (2.0.0-2) unstable; urgency=medium
+
+  * Team upload.
+  * Check existence of files before calling chmod on them to fix arch indep
+    builds
+    Closes: #904444
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * Clean up properly
+  * Fix paths in d/copyright
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Sun, 05 Aug 2018 02:22:58 +0200
+
 trnascan-se (2.0.0-1) unstable; urgency=medium
 
   [ Steffen Moeller ]

debian/clean

+tRNAscan-SE.conf

debian/control

 Source: trnascan-se
-Section: non-free/science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Afif Elghraoui <afif@debian.org>
+Section: non-free/science
+XS-Autobuild: no
+Priority: optional
 Build-Depends: debhelper (>= 11)
-Standards-Version: 4.1.3
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se
+Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git
 Homepage: http://lowelab.ucsc.edu/tRNAscan-SE
-Vcs-Git: https://anonscm.debian.org/git/debian-med/trnascan-se.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trnascan-se.git
 
 Package: trnascan-se
 Architecture: any
-Depends:
-	${shlibs:Depends},
+Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${perl:Depends},
          trnascan-se-common (= ${source:Version}),
-	infernal (>= 1.0),
+         infernal
 Description: detection of transfer RNA genes in genomic sequence
  tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while
  giving less than one false positive per 15 gigabases. Two previously described
@@ -30,8 +30,7 @@ Description: detection of transfer RNA genes in genomic sequence
 
 Package: trnascan-se-common
 Architecture: all
-Depends:
-	${misc:Depends},
+Depends: ${misc:Depends},
          ${perl:Depends}
 Description: detection of transfer RNA genes in genomic sequence (common files)
  tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while

debian/copyright

@@ -11,23 +11,23 @@ Copyright:
 	2017 Brian Lin
 License: GPL-3.0+
 
-Files: dbmalloc.h
+Files: src/dbmalloc.h
 Copyright: 1990-1992 Conor P. Cahill
 License: Cahill
  You may copy, distribute, and use this software as long as this
  copyright statement is not removed.
 
-Files: gnuregex.*
+Files: src/gnuregex.*
 Copyright: 1985, 1989-1993 Free Software Foundation, Inc.
 License: GPL-2.0+
 
-Files: sqio.c
+Files: src/sqio.c
 Copyright:
 	1990 Don Gilbert <gilbertd@bio.indiana.edu>
 	1992-1996 Sean R. Eddy
 License: GPL-2.0+
 
-Files: trnascan.c
+Files: src/trnascan.c
 Copyright: 1991 The Regents of the University of California
 License: UC
  This software was produced by the Los Alamos National Laboratory,
@@ -41,10 +41,6 @@ License: UC
  express or implied, or assumes any liability or responsibility
  for the use of this software.
 
-Files: Cove/*
-Copyright: 1993-1994 Sean R. Eddy
-License: GPL-2.0+
-
 Files: debian/*
 Copyright: 2015-2018 Afif Elghraoui <afif@debian.org>
 License: GPL-2.0+

debian/patches/chmod_only_if_exists.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sat, 04 Aug 2018 15:15:12 +0200
+Bug-Debian: https://bugs.debian.org/904444
+Description: Check existence of files before calling chmod on them to fix arch indep builds
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -52,15 +52,15 @@ tRNAscan-SE.conf: tRNAscan-SE.conf.src M
+ 
+ bin/sstofa: src/sstofa.in Makefile
+ 	$(do_subst) < $(srcdir)/src/sstofa.in > bin/sstofa
+-	chmod +x bin/sstofa
++	if [ -x bin/sstofa ] ; then chmod +x bin/sstofa ; fi
+ 
+ bin/fasta2gsi: src/fasta2gsi.in Makefile
+ 	$(do_subst) < $(srcdir)/src/fasta2gsi.in > bin/fasta2gsi
+-	chmod +x bin/fasta2gsi
++	if [ -x bin/fasta2gsi ] ; then chmod +x bin/fasta2gsi ; fi
+ 
+ bin/EukHighConfidenceFilter: EukHighConfidenceFilter.in Makefile
+ 	$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
+-	chmod +x bin/EukHighConfidenceFilter
++	if [ -x bin/EukHighConfidenceFilter ] ; then chmod +x bin/EukHighConfidenceFilter ; fi
+ 
+ # copy data libraries
+ install-data-hook:

debian/patches/series

 pkg-data.patch
 confdir.patch
+chmod_only_if_exists.patch

debian/rules

 #!/usr/bin/make -f
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@