Index: Makefile
===================================================================
--- Makefile	(revision 400058)
+++ Makefile	(working copy)
@@ -2,16 +2,32 @@
 # $FreeBSD$
 
 PORTNAME=	gmap
-PORTVERSION=	2006.04.21
-PORTREVISION=	1
+PORTVERSION=	2015.09.21
 CATEGORIES=	biology
 MASTER_SITES=	http://research-pub.gene.com/gmap/src/
-DISTNAME=	${PORTNAME}-${PORTVERSION:C|\.|-|g}
+DISTNAME=	${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g}
 
 MAINTAINER=	rpz@cse.wustl.edu
 COMMENT=	Genomic Mapping and Alignment Program for mRNA and EST Sequences
 
+LICENSE=	GMAP
+LICENSE_NAME=	GMAP License
+LICENSE_FILE=	${WRKSRC}/COPYING
+LICENSE_PERMS=	dist-mirror pkg-mirror auto-accept
+
 USES=		gmake perl5
 GNU_CONFIGURE=	yes
 
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C|\.|-|g}
+
+OPTIONS_DEFINE=	SIMD
+
+SIMD_CONFIGURE_OFF=	--disable-builtin-popcount --disable-simd
+
+# shebang_fix operates during patch.
+# These scripts are created during configure.
+post-configure:
+	${REINPLACE_CMD} -e 's|/usr/bin/perl|${PERL}|g' \
+		${WRKSRC}/Makefile ${WRKSRC}/util/*.pl
+
 .include <bsd.port.mk>
Index: distinfo
===================================================================
--- distinfo	(revision 400058)
+++ distinfo	(working copy)
@@ -1,2 +1,2 @@
-SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984
-SIZE (gmap-2006-04-21.tar.gz) = 1282409
+SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
+SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019
Index: files/patch-configure
===================================================================
--- files/patch-configure	(revision 400058)
+++ files/patch-configure	(nonexistent)
@@ -1,11 +0,0 @@
---- configure.orig	Mon Sep 25 21:06:11 2006
-+++ configure	Mon Sep 25 21:05:13 2006
-@@ -3365,7 +3365,7 @@
- else
-   answer=""
- fi;
--if test x"$answer" == x; then
-+if test x"$answer" = x; then
- 
-   EXP_VAR=GMAPDB
-   FROM_VAR='${prefix}/share'

Property changes on: files/patch-configure
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: pkg-message
===================================================================
--- pkg-message	(nonexistent)
+++ pkg-message	(working copy)
@@ -0,0 +1,7 @@
+NOTE:
+
+The default configuration for the gmap port disables all optimizations
+to maintain compatibility with the widest range of systems.
+
+To get a binary optimized for your system please deinstall gmap and
+build from ports using "make config" to enable the SIMD option.

Property changes on: pkg-message
___________________________________________________________________
Added: fbsd:nokeywords
## -0,0 +1 ##
+yes
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Index: pkg-plist
===================================================================
--- pkg-plist	(revision 400058)
+++ pkg-plist	(working copy)
@@ -1,12 +1,35 @@
+bin/atoiindex
+bin/cmetindex
+bin/dbsnp_iit
+bin/ensembl_genes
+bin/fa_coords
+bin/get-genome
+bin/gff3_genes
+bin/gff3_introns
+bin/gff3_splicesites
 bin/gmap
-bin/get-genome
+bin/gmap_build
+bin/gmap_compress
+bin/gmap_process
+bin/gmap_reassemble
+bin/gmap_uncompress
 bin/gmapindex
+bin/gmapl
+bin/gsnap
+bin/gsnapl
+bin/gtf_genes
+bin/gtf_introns
+bin/gtf_splicesites
+bin/gvf_iit
+bin/iit_dump
+bin/iit_get
 bin/iit_store
-bin/iit_get
-bin/iit_dump
-bin/gmap_compress
-bin/gmap_uncompress
-bin/gmap_process
-bin/gmap_setup
 bin/md_coords
-bin/fa_coords
+bin/psl_genes
+bin/psl_introns
+bin/psl_splicesites
+bin/sam_sort
+bin/snpindex
+bin/uniqscan
+bin/uniqscanl
+bin/vcf_iit