5 files changed, 60 insertions, 25 deletions

diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile
index 1f4d6e061857..0360a1a6d8f1 100644
--- a/biology/gmap/Makefile
+++ b/biology/gmap/Makefile
@@ -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
+MAINTAINER=	jwbacon@tds.net
 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 ${WRKSRC}/util/*.pl
+
 .include <bsd.port.mk>
diff --git a/biology/gmap/distinfo b/biology/gmap/distinfo
index d5ad5ea321c9..07ef00669c29 100644
--- a/biology/gmap/distinfo
+++ b/biology/gmap/distinfo
@@ -1,2 +1,2 @@
-SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984
-SIZE (gmap-2006-04-21.tar.gz) = 1282409
+SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
+SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019
diff --git a/biology/gmap/files/patch-configure b/biology/gmap/files/patch-configure
deleted file mode 100644
index e4144329cb3b..000000000000
--- a/biology/gmap/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	Mon Sep 25 21:06:11 2006
-+++ configure	Mon Sep 25 21:05:13 2006
-@@ -3365,7 +3365,7 @@
- else
-   answer=""
- fi;
--if test x"$answer" == x; then
-+if test x"$answer" = x; then
- 
-   EXP_VAR=GMAPDB
-   FROM_VAR='${prefix}/share'
diff --git a/biology/gmap/pkg-message b/biology/gmap/pkg-message
new file mode 100644
index 000000000000..23a7dd1e50af
--- /dev/null
+++ b/biology/gmap/pkg-message
@@ -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.
diff --git a/biology/gmap/pkg-plist b/biology/gmap/pkg-plist
index 83108a3b8677..ec7d83f2035a 100644
--- a/biology/gmap/pkg-plist
+++ b/biology/gmap/pkg-plist
@@ -1,12 +1,35 @@
-bin/gmap
+bin/atoiindex
+bin/cmetindex
+bin/dbsnp_iit
+bin/ensembl_genes
+bin/fa_coords
 bin/get-genome
-bin/gmapindex
-bin/iit_store
-bin/iit_get
-bin/iit_dump
+bin/gff3_genes
+bin/gff3_introns
+bin/gff3_splicesites
+bin/gmap
+bin/gmap_build
 bin/gmap_compress
-bin/gmap_uncompress
 bin/gmap_process
-bin/gmap_setup
+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/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