biology/stacks: Upgrade to 2.3

Approved by:    jrm (mentor, implicit)

biology/stacks/Makefile

@@ -1,9 +1,8 @@
 # $FreeBSD$
 
 PORTNAME=	stacks
-DISTVERSION=	1.48
-PORTREVISION=	3
-CATEGORIES=	biology
+DISTVERSION=	2.3
+CATEGORIES=	biology perl5 python
 MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -13,7 +12,9 @@ LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		compiler:openmp gmake python shebangfix
-SHEBANG_FILES=	scripts/*.pl scripts/*.py
+
+SHEBANG_FILES=	scripts/*.pl scripts/*.py \
+		scripts/stacks-integrate-alignments scripts/stacks-gdb
 GNU_CONFIGURE=	yes
 
 LDFLAGS+=	-lpthread
@@ -21,7 +22,7 @@ LDFLAGS+=	-lpthread
 .include <bsd.port.pre.mk>
 
 .if ${ARCH} != amd64 && ${ARCH} != i386
-USE_GCC=        yes
+USE_GCC=	yes
 .endif
 
 .include <bsd.port.post.mk>

biology/stacks/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1520376299
-SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e
-SIZE (stacks-1.48.tar.gz) = 895195
+TIMESTAMP = 1547306940
+SHA256 (stacks-2.3.tar.gz) = 2a5befaf11ca2f191afcd42a3a3392290d6a116d7fe737b69a2c4d5b77f40c99
+SIZE (stacks-2.3.tar.gz) = 10962586

biology/stacks/files/patch-htslib_Makefile

@@ -1,20 +0,0 @@
---- htslib/Makefile.orig	2016-09-16 15:40:03 UTC
-+++ htslib/Makefile
-@@ -22,13 +22,13 @@
- # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- # DEALINGS IN THE SOFTWARE.
- 
--CC     = gcc
--AR     = ar
--RANLIB = ranlib
-+CC     ?= gcc
-+AR     ?= ar
-+RANLIB ?= ranlib
- 
- CPPFLAGS =
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
--CFLAGS   = -g -Wall -O2
-+CFLAGS   ?= -g -Wall -O2
- EXTRA_CFLAGS_PIC = -fpic
- LDFLAGS  =
- LIBS     =

biology/stacks/pkg-plist

@@ -2,24 +2,19 @@ bin/clone_filter
 bin/count_fixed_catalog_snps.py
 bin/cstacks
 bin/denovo_map.pl
-bin/exec_velvet.pl
-bin/export_sql.pl
-bin/genotypes
-bin/index_radtags.pl
+bin/gstacks
 bin/integrate_alignments.py
 bin/kmer_filter
-bin/load_radtags.pl
-bin/load_sequences.pl
 bin/phasedstacks
 bin/populations
 bin/process_radtags
 bin/process_shortreads
-bin/pstacks
 bin/ref_map.pl
-bin/rxstacks
-bin/sort_read_pairs.pl
 bin/sstacks
-bin/stacks_export_notify.pl
+bin/stacks-dist-extract
+bin/stacks-gdb
+bin/stacks-integrate-alignments
+bin/tsv2bam
 bin/ustacks
 %%DATADIR%%/php/CatalogClass.php
 %%DATADIR%%/php/Locus.php