debian/changelog

 trinityrnaseq (2.6.6+dfsg-1) UNRELEASED; urgency=medium
 
+  * Team upload.
+
   [ Michael R. Crusoe ]
   * New upstream release, now with the sample data returned
     Closes: #897877
   * Build and ship seqtk-trinity
 
-  TODO: update salmon to v0.9; required for this version
-
   [ Andreas Tille ]
   * debhelper 11
   * Point Vcs fields to salsa.debian.org
-  * Standards-Version: 4.1.5
+  * Standards-Version: 4.2.1
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+  * Fix permissions and Perl interpreter path
 
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 17 Feb 2018 07:38:23 -0800
 

debian/control

@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                jellyfish,
                salmon,
                zlib1g-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
 Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
 Homepage: http://trinityrnaseq.github.io/

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Trinity
 Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.3.tar.gz
 Files-Excluded:  util/support_scripts/*.jar

debian/rules

@@ -38,8 +38,10 @@ override_dh_auto_clean:
 	cd trinity-plugins && $(MAKE) clean || true
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	java -cp Butterfly.jar TransAssembly_allProbPaths -N 10000 -L 300 \
 		-F 300 -C Butterfly/src/sample_data/c1.graph --stderr -V 20
+endif
 
 override_dh_auto_install:
 	for target in ${SOURCE_DIRECTORIES_ALL}; do dh_auto_install \
@@ -66,3 +68,9 @@ override_dh_install-indep:
 		${EXBASEDIR}/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/runMe.sh \
 		${EXBASEDIR}/trinity_ext_sample_data/test_Inchworm/runMe_MPI.sh \
 
+override_dh_fixperms:
+	dh_fixperms
+	find debian -name genwig.sh -exec chmod +x \{\} \;
+	for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
+	done