Afif Elghraoui · Afif Elghraoui · Afif Elghraoui · Afif Elghraoui · Afif Elghraoui · Afif Elghraoui
--- a/debian/changelog
+++ b/debian/changelog
-trnascan-se (2.0.0-1) UNRELEASED; urgency=medium
+trnascan-se (2.0.0-1) unstable; urgency=medium

  [ Steffen Moeller ]
  * debian/upstream/metadata:
@@ -8,12 +8,17 @@ trnascan-se (2.0.0-1) UNRELEASED; urgency=medium

  [ Afif Elghraoui ]
  * debian/watch: update to new URL
-  * New upstream version 2.0.0
+  * New upstream version
  * Standards-Version 4.1.3
  * debhelper compat 11
  * d/rules: clean up and remove dh_installchangelogs
+  * Overhaul packaging for new build system
+  * d/copyright: license change (GPL 2+ -> 3+); updated copyright years
+  * install examples
+  * Add dependency on infernal
+  * Update autopkgtest

- -- Afif Elghraoui <afif@debian.org>  Mon, 19 Feb 2018 17:26:27 -0500
+ -- Afif Elghraoui <afif@debian.org>  Sat, 24 Feb 2018 22:18:01 -0500

 trnascan-se (1.3.1-1) unstable; urgency=medium


--- a/debian/control
+++ b/debian/control
@@ -15,9 +15,8 @@ Depends:
 	${shlibs:Depends},
 	${misc:Depends},
 	${perl:Depends},
-	trnascan-se-common (= ${source:Version})
-Suggests:
-	infernal (>= 1.0)
+	trnascan-se-common (= ${source:Version}),
+	infernal (>= 1.0),
 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

--- a/debian/copyright
+++ b/debian/copyright
@@ -6,9 +6,10 @@ Source: http://lowelab.ucsc.edu/software/
 Files: *
 Copyright:
 	1992-1996 Sean R. Eddy
-	1992-1996, 2011 Todd M.J. Lowe
-	2011 Patricia Chan
-License: GPL-2.0+
+	1992-1996, 2011-2017 Todd M.J. Lowe
+	2011-2017 Patricia Chan
+	2017 Brian Lin
+License: GPL-3.0+

 Files: dbmalloc.h
 Copyright: 1990-1992 Conor P. Cahill
@@ -45,7 +46,7 @@ Copyright: 1993-1994 Sean R. Eddy
 License: GPL-2.0+

 Files: debian/*
-Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
+Copyright: 2015-2018 Afif Elghraoui <afif@debian.org>
 License: GPL-2.0+

 License: GPL-2.0+
@@ -64,3 +65,20 @@ License: GPL-2.0+
 .
 On Debian systems, the complete text of the GNU General
 Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+License: GPL-3.0+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-3".
--- a/debian/examples
+++ b/debian/examples
+Demo/*
--- a/debian/patches/confdir.patch
+++ b/debian/patches/confdir.patch
+Description: install default config file into /etc instead of /usr/bin
+Author: Afif Elghraoui <afif@debian.org>
+Forwarded: no
+Last-Update: 2018-02-24
+--- trnascan-se.orig/tRNAscan-SE.src
+++ trnascan-se/tRNAscan-SE.src
+@@ -44,7 +44,7 @@
+ our $program_id = "tRNAscan-SE-".$version;
+ 
+ # modified by 'make'
+-our $default_conf = "@bindir@/tRNAscan-SE.conf";
+our $default_conf = "@sysconfdir@/tRNAscan-SE.conf";
+ 
+ # Signal handling
+ $SIG{'TERM'} = 'error_handler';
+--- trnascan-se.orig/Makefile.am
+++ trnascan-se/Makefile.am
+@@ -28,11 +28,12 @@
+ bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
+ 
+ # process scripts
+-# treat tRNAscan-SE.conf as a script since it's just easier
+-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE
+# config file
+dist_sysconf_DATA = tRNAscan-SE.conf
+ # for a few files, need to substitute perl path, bin directory, and lib directory
+ # first, define a function for it
+-do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@pkgdatadir\@,$(pkgdatadir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' 
+do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@pkgdatadir\@,$(pkgdatadir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' -e 's,\@sysconfdir\@,$(sysconfdir),g'
+ 
+ # extra steps for cleaning/distribution
+ CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
--- a/debian/patches/pkg-data.patch
+++ b/debian/patches/pkg-data.patch
 Description: use pkgdatadir and DESTDIR in install-data-hook
- omitting DESTDIR causes build problems, and pkgdatadir is more appropriate
- than libdir for these file types.
+ * omitting DESTDIR causes build problems
+ * pkgdatadir is more appropriate than libdir for these file types.
+ * Paths are all off because of using the Perl module subdirectory (tRNAscan-SE)
+   as the base data directory to search from
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: no
 Last-Update: 2018-02-24
@@ -11,7 +13,7 @@ Last-Update: 2018-02-24
 bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND)
 bin_trnascan_1_4_SOURCES = src/trnascan.c
 -bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
-+bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(pkgdatadir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
+bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(pkgdatadir)\/models\"  $(AM_CFLAGS)
 bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
 bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
 
@@ -45,3 +47,36 @@ Last-Update: 2018-02-24
 +	test -d $(DESTDIR)/$(pkgdatadir) || mkdir -p $(DESTDIR)/$(pkgdatadir)
 +	chmod u+w $(DESTDIR)/$(pkgdatadir)
 +	cp -rf $(srcdir)/lib/* $(DESTDIR)/$(pkgdatadir)
+--- trnascan-se.orig/tRNAscan-SE.src
+++ trnascan-se/tRNAscan-SE.src
+@@ -18,7 +18,7 @@
+ #                           
+ 
+ use strict;
+-use lib "@libdir@/tRNAscan-SE";
+use lib "@pkgdatadir@";
+ use Getopt::Long;
+ use tRNAscanSE::Configuration;
+ use tRNAscanSE::tRNA;
+--- trnascan-se.orig/EukHighConfidenceFilter.in
+++ trnascan-se/EukHighConfidenceFilter.in
+@@ -13,7 +13,7 @@
+ # --------------------------------------------------------------------
+  
+ use strict;
+-use lib "@libdir@/tRNAscan-SE";
+use lib "@pkgdatadir@";
+ use Getopt::Long;
+ 
+ use tRNAscanSE::tRNA;
+--- trnascan-se.orig/tRNAscan-SE.conf.src
+++ trnascan-se/tRNAscan-SE.conf.src
+@@ -3,7 +3,7 @@
+ 
+ # default paths
+ bin_dir: @bindir@
+-lib_dir: @libdir@/tRNAscan-SE
+lib_dir: @pkgdatadir@
+ infernal_dir: {bin_dir}
+ 
+ # temporary files
--- a/debian/patches/series
+++ b/debian/patches/series
 pkg-data.patch
+confdir.patch
--- a/debian/rules
+++ b/debian/rules
@@ -2,3 +2,7 @@

 %:
 	dh $@
+
+# tRNAscan can't handle compressed fasta files
+override_dh_compress:
+	dh_compress -X .fa
--- a/debian/tests/control
+++ b/debian/tests/control
-Test-Command: make testrun
+Tests: rules
 Depends: @
 Restrictions: allow-stderr
--- a/debian/tests/rules
+++ b/debian/tests/rules
+#!/bin/sh
+
+examples=/usr/share/doc/trnascan-se/examples
+
+cd $AUTOPKGTEST_TMP
+
+tRNAscan-SE -d -y -o testrun.out ${examples}/Example1.fa
--- a/debian/trnascan-se.install
+++ b/debian/trnascan-se.install
 usr/bin
+etc