debian/changelog

+transdecoder (5.0.1-2) unstable; urgency=medium
+
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+  * Fix Perl path
+
+ -- Andreas Tille <tille@debian.org>  Tue, 30 Oct 2018 14:25:40 +0100
+
 transdecoder (5.0.1-1) unstable; urgency=medium
 
   * New upstream version (no need to repackage since binary files are now

debian/control

@@ -6,9 +6,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                liburi-perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/transdecoder.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
+Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
 Homepage: https://transdecoder.github.io/
 
 Package: transdecoder

debian/patches/fix-test

-Author: Michael R. Crusoe <michael.crusoe@gmail.com>
-Description: Fix tests
---- transdecoder.orig/Makefile
-+++ transdecoder/Makefile
-@@ -8,6 +8,7 @@
- 	cd ./sample_data && ./cleanme.pl
- 
- test:
--	cd ./sample_data/ && ./runMe.sh
--
-+	cd sample_data/cufflinks_example && ./runMe.sh
-+	cd sample_data/pasa_example && ./runMe.sh
-+	cd sample_data/simple_transcriptome_target && ./runMe.sh
- 

debian/rules

@@ -13,8 +13,10 @@ override_dh_auto_clean:
 override_dh_auto_build:
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test
 	cd ./sample_data && for script in ./*/cleanme.pl; do $$($$script); done
+endif
 
 override_dh_install:
 	dh_install
@@ -39,3 +41,9 @@ override_dh_fixperms:
 override_dh_clean:
 	# generated man pages
 	dh_clean debian/TransDecoder.LongOrfs.1 debian/TransDecoder.Predict.1
+
+override_dh_installdocs:
+	dh_installdocs
+	for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done