debian/changelog

 trinityrnaseq (2.6.6+dfsg-1) UNRELEASED; urgency=medium
 
+  [ 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
+
  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 17 Feb 2018 07:38:23 -0800
 
 trinityrnaseq (2.5.1+dfsg-2) unstable; urgency=medium

debian/compat

-10
+11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                jellyfish (>= 2.1.4),
                libjung-free-java,
                javahelper,
@@ -17,9 +17,9 @@ Build-Depends: debhelper (>= 10),
                jellyfish,
                salmon,
                zlib1g-dev
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trinityrnaseq.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/trinityrnaseq.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq
+Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git
 Homepage: http://trinityrnaseq.github.io/
 
 Package: trinityrnaseq

debian/patches/assume_modern_g++.patch

+From: Brian Haas <brianjohnhaas@gmail.com>
+Date: Mon, 5 Feb 2018 19:51:50 -0500
+Origin: https://github.com/trinityrnaseq/trinityrnaseq/commit/a3d279c17f868fd51d56f8e1a6f9a3c223480fbf.patch
+Bug-Debian: https://bugs.debian.org/897877
+Subject: [PATCH] assume modern g++
+
+---
+ Chrysalis/Makefile | 16 +---------------
+ 1 file changed, 1 insertion(+), 15 deletions(-)
+
+diff --git a/Chrysalis/Makefile b/Chrysalis/Makefile
+index 346dc5c9..1f1a4223 100644
+--- a/Chrysalis/Makefile
++++ b/Chrysalis/Makefile
+@@ -297,21 +297,7 @@ SYS_INCS = -I.
+ 
+ # Where to find system-specific includes:
+ ifeq ($(COMPILER),g++)
+-  ifeq ($(GPP_MAJOR_VERSION),2)
+-       SYS_INCS	= -I. -I- $(XERCES_INC)
+-  endif
+-  ifeq ($(GPP_MAJOR_VERSION),3)
+-       SYS_INCS	= -I. -I- $(XERCES_INC)
+-  endif
+-  ifeq ($(GPP_MAJOR_VERSION),4)
+-       SYS_INCS	= -iquote . $(XERCES_INC)
+-  endif
+-  ifeq ($(GPP_MAJOR_VERSION),5)
+-       SYS_INCS        = -iquote . $(XERCES_INC)
+-  endif
+-  ifeq ($(GPP_MAJOR_VERSION),6)
+-       SYS_INCS        = -iquote . $(XERCES_INC)
+-  endif
++	SYS_INCS        = -iquote . $(XERCES_INC)
+ endif
+ 
+ # Linking control (e.g. to link templates):

debian/patches/series

@@ -10,3 +10,4 @@ adjust-trimmomatic-adapters-path
 build_with_gcc6.patch
 NeedlemanWunschGotohBanded.patch
 disable-libieee
+# assume_modern_g++.patch