bowtie2: Fix bash dep and respect CXXFLAGS

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jan 21 07:38:40 2021 -0600
Changeset:	d5879dda60a843fce916b4f5e9484850e05bebcf

Modified Files:
	bowtie2/Makefile
	bowtie2/distinfo
	bowtie2/patches/patch-Makefile
Added Files:
	bowtie2/patches/patch-scripts_bowtie2-hbb.sh

Log Message:
bowtie2: Fix bash dep and respect CXXFLAGS

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d5879dda60a843fce916b4f5e9484850e05bebcf

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bowtie2/Makefile                             |  1 +
 bowtie2/distinfo                             |  3 ++-
 bowtie2/patches/patch-Makefile               | 13 +++++++++++--
 bowtie2/patches/patch-scripts_bowtie2-hbb.sh | 15 +++++++++++++++
 4 files changed, 29 insertions(+), 3 deletions(-)

diffs:
diff --git a/bowtie2/Makefile b/bowtie2/Makefile
index 9b28696662..ffe68b4764 100644
--- a/bowtie2/Makefile
+++ b/bowtie2/Makefile
@@ -14,6 +14,7 @@ USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake pax:build perl:run
 REPLACE_PERL=	scripts/*.pl bowtie2
 REPLACE_PYTHON=	bowtie2-build bowtie2-inspect
+REPLACE_SH=	scripts/bowtie2-hbb.sh
 
 # Use onetbb on supported platforms when a package is available
 MAKE_FLAGS+=	NO_TBB=1
diff --git a/bowtie2/distinfo b/bowtie2/distinfo
index 492bc07979..ce3467113f 100644
--- a/bowtie2/distinfo
+++ b/bowtie2/distinfo
@@ -4,4 +4,5 @@ SHA1 (bowtie2-2.4.2.tar.gz) = b8eb8158828459412586003b6051d79ed123fc82
 RMD160 (bowtie2-2.4.2.tar.gz) = 0c6c5fe29a40f913e3810d1fe022b948403dfb09
 SHA512 (bowtie2-2.4.2.tar.gz) = f8bb74aaec7557bcd1bc4b5ec5e2a3b141d78c88b04f39cdcc417d15f058bdb48b15d159c4ab569b4d655e3d1bd0cf8152343f05b9a20d5d29680c3e8c2f1a05
 Size (bowtie2-2.4.2.tar.gz) = 10590144 bytes
-SHA1 (patch-Makefile) = 041f35da8bccdf6d7c3bfe4306992e04b6a7c516
+SHA1 (patch-Makefile) = 00aa2794474478aa578f6aee5cdb319dfa132ae1
+SHA1 (patch-scripts_bowtie2-hbb.sh) = d360774cfef0675b4c1cdd1175b394d2cf7f761a
diff --git a/bowtie2/patches/patch-Makefile b/bowtie2/patches/patch-Makefile
index 8f72363b20..3df5976ffa 100644
--- a/bowtie2/patches/patch-Makefile
+++ b/bowtie2/patches/patch-Makefile
@@ -1,8 +1,8 @@
 $NetBSD$
 
-# Respect PREFIX
+# Respect PREFIX and CXXFLAGS
 
---- Makefile.orig	2021-01-21 00:03:29.754913712 +0000
+--- Makefile.orig	2020-10-06 03:46:41.000000000 +0000
 +++ Makefile
 @@ -21,7 +21,7 @@
  # Makefile for bowtie, bowtie2-build, bowtie2-inspect
@@ -13,3 +13,12 @@ $NetBSD$
  bindir := $(PREFIX)/bin
  
  ARCH := $(shell uname -m)
+@@ -234,7 +234,7 @@ ifeq (32,$(BITS))
+ endif
+ 
+ DEBUG_FLAGS    := -O0 -g3 $(SSE_FLAG)
+-RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
++# RELEASE_FLAGS  := -O3 $(SSE_FLAG) -funroll-loops -g3
+ NOASSERT_FLAGS := -DNDEBUG
+ FILE_FLAGS     := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
diff --git a/bowtie2/patches/patch-scripts_bowtie2-hbb.sh b/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
new file mode 100644
index 0000000000..baa29cb3a9
--- /dev/null
+++ b/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Eliminate bash dependency
+
+--- scripts/bowtie2-hbb.sh.orig	2020-10-06 03:46:41.000000000 +0000
++++ scripts/bowtie2-hbb.sh
+@@ -11,7 +11,7 @@ while getopts "sb:" opt; do
+ done
+ shift $(($OPTIND - 1))
+ 
+-if [ "$branch" == "" ] ; then
++if [ "$branch" = "" ] ; then
+     branch="master"
+ fi
+