Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA

and EST Sequences.

PR:		ports/103651
Submitted by:	Bob Zimmermann <rpz at cse.wustl.edu>

8 files changed, 105 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 69f946bebccb..f41a9a4fd496 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -30,6 +30,7 @@
     SUBDIR += garlic
     SUBDIR += genpak
     SUBDIR += gff2ps
+    SUBDIR += gmap
     SUBDIR += gperiodic
     SUBDIR += grappa
     SUBDIR += hmmer
diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile
new file mode 100644
index 000000000000..f1414a8839ad
--- /dev/null
+++ b/biology/gmap/Makefile
@@ -0,0 +1,32 @@
+# Ports collection makefile for:   gmap
+# Date created:        24 September 2006
+# Whom:                Bob Zimmermann <rpz@cse.wustl.edu>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	gmap
+PORTVERSION=	2006.04.21
+CATEGORIES=	biology
+MASTER_SITES=	http://www.gene.com/share/gmap/src/
+DISTNAME=	${PORTNAME}-${PORTVERSION:C|\.|-|g}
+
+MAINTAINER=	rpz@cse.wustl.edu
+COMMENT=	A Genomic Mapping and Alignment Program for mRNA and EST Sequences
+
+FETCH_DEPENDS=	${LOCALBASE}/bin/wget:${PORTSDIR}/ftp/wget
+
+FETCH_CMD=	${LOCALBASE}/bin/wget
+FETCH_BEFORE_ARGS=	--no-check-certificate
+DISABLE_SIZE=	yes
+USE_GMAKE=	yes
+GNU_CONFIGURE=	yes
+CONFIGURE_TARGET=--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+
+.include <bsd.port.pre.mk>
+
+.if ${OSVERSION} < 500036
+EXTRA_PATCHES+=	${PATCHDIR}/extra-*
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/biology/gmap/distinfo b/biology/gmap/distinfo
new file mode 100644
index 000000000000..59bf340d55fc
--- /dev/null
+++ b/biology/gmap/distinfo
@@ -0,0 +1,3 @@
+MD5 (gmap-2006-04-21.tar.gz) = 197a47e30dac77c93d3f1b99ec805217
+SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984
+SIZE (gmap-2006-04-21.tar.gz) = 1282409
diff --git a/biology/gmap/files/extra-patch-src-genome.c b/biology/gmap/files/extra-patch-src-genome.c
new file mode 100644
index 000000000000..bea815b97d43
--- /dev/null
+++ b/biology/gmap/files/extra-patch-src-genome.c
@@ -0,0 +1,17 @@
+--- src/genome.c.orig	Sun Mar  5 11:14:48 2006
++++ src/genome.c	Fri Sep 29 09:23:15 2006
+@@ -15,13 +15,13 @@
+ #include <stddef.h>
+ #include <stdlib.h>
+ #include <string.h>
+-#include <sys/mman.h>		/* For munmap */
+ #ifdef HAVE_UNISTD_H
+ #include <unistd.h>		/* For lseek and close */
+ #endif
+ #ifdef HAVE_SYS_TYPES_H
+ #include <sys/types.h>		/* For off_t */
+ #endif
++#include <sys/mman.h>		/* For munmap */
+ 
+ #ifdef HAVE_PTHREAD
+ #include <pthread.h>		/* sys/types.h already included above */
diff --git a/biology/gmap/files/extra-patch-src-indexdb.c b/biology/gmap/files/extra-patch-src-indexdb.c
new file mode 100644
index 000000000000..63ff76d37e8b
--- /dev/null
+++ b/biology/gmap/files/extra-patch-src-indexdb.c
@@ -0,0 +1,17 @@
+--- src/indexdb.c.orig	Sat Mar  4 10:19:53 2006
++++ src/indexdb.c	Fri Sep 29 11:12:55 2006
+@@ -22,13 +22,13 @@
+ #include <stdlib.h>
+ #include <string.h>		/* For memset */
+ #include <ctype.h>		/* For toupper */
+-#include <sys/mman.h>		/* For munmap */
+ #ifdef HAVE_UNISTD_H
+ #include <unistd.h>		/* For lseek and close */
+ #endif
+ #ifdef HAVE_SYS_TYPES_H
+ #include <sys/types.h>		/* For off_t */
+ #endif
++#include <sys/mman.h>		/* For munmap */
+ 
+ #include "mem.h"
+ #include "fopen.h"
diff --git a/biology/gmap/files/patch-configure b/biology/gmap/files/patch-configure
new file mode 100644
index 000000000000..e4144329cb3b
--- /dev/null
+++ b/biology/gmap/files/patch-configure
@@ -0,0 +1,11 @@
+--- 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-descr b/biology/gmap/pkg-descr
new file mode 100644
index 000000000000..d09d51fed649
--- /dev/null
+++ b/biology/gmap/pkg-descr
@@ -0,0 +1,12 @@
+A standalone program for mapping and aligning cDNA sequences to a
+genome. The program maps and aligns a single sequence with minimal
+startup time and memory requirements, and provides fast batch
+processing of large sequence sets. The program generates accurate
+gene structures, even in the presence of substantial polymorphisms
+and sequence errors, without using probabilistic splice site models.
+Methodology underlying the program includes a minimal sampling
+strategy for genomic mapping, oligomer chaining for approximate
+alignment, sandwich DP for splice site detection, and microexon
+identification with statistical significance testing.
+
+WWW: http://www.gene.com/share/gmap
diff --git a/biology/gmap/pkg-plist b/biology/gmap/pkg-plist
new file mode 100644
index 000000000000..83108a3b8677
--- /dev/null
+++ b/biology/gmap/pkg-plist
@@ -0,0 +1,12 @@
+bin/gmap
+bin/get-genome
+bin/gmapindex
+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