Attachment #162406 for bug #203334




# $FreeBSD$

PORTNAME=	gmap
PORTVERSION=	2015.09.21
PORTREVISION=	1
CATEGORIES=	biology
MASTER_SITES=	http://research-pub.gene.com/gmap/src/
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>

Lines 1-2 Link Here

(-)distinfo (-2 / +2 lines)
1	SHA256 (gmap-2006-04-21.tar.gz) = e635884c07d57e9a79e6e6744587dc1459dd0895eb40d6ca4b61f9827e332984	1	SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
2	SIZE (gmap-2006-04-21.tar.gz) = 1282409	2	SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019

Lines 1-11 Link Here

(-)files/patch-configure (-11 lines)
1	--- configure.orig Mon Sep 25 21:06:11 2006
2	+++ configure Mon Sep 25 21:05:13 2006
3	@@ -3365,7 +3365,7 @@
4	else
5	answer=""
6	fi;
7	-if test x"$answer" == x; then
8	+if test x"$answer" = x; then
9
10	EXP_VAR=GMAPDB
11	FROM_VAR='${prefix}/share'

Line 0 Link Here

(-)pkg-message (+7 lines)
	1	NOTE:
	2
	3	The default configuration for the gmap port disables all optimizations
	4	to maintain compatibility with the widest range of systems.
	5
	6	To get a binary optimized for your system please deinstall gmap and
	7	build from ports using "make config" to enable the SIMD option.

Lines 1-12 Link Here

(-)pkg-plist (-8 / +31 lines)
		1	bin/atoiindex
		2	bin/cmetindex
		3	bin/dbsnp_iit
		4	bin/ensembl_genes
		5	bin/fa_coords
		6	bin/get-genome
		7	bin/gff3_genes
		8	bin/gff3_introns
		9	bin/gff3_splicesites
1	bin/gmap	10	bin/gmap
2	bin/get-genome	11	bin/gmap_build
		12	bin/gmap_compress
		13	bin/gmap_process
		14	bin/gmap_reassemble
		15	bin/gmap_uncompress
3	bin/gmapindex	16	bin/gmapindex
		17	bin/gmapl
		18	bin/gsnap
		19	bin/gsnapl
		20	bin/gtf_genes
		21	bin/gtf_introns
		22	bin/gtf_splicesites
		23	bin/gvf_iit
		24	bin/iit_dump
		25	bin/iit_get
4	bin/iit_store	26	bin/iit_store
5	bin/iit_get
6	bin/iit_dump
7	bin/gmap_compress
8	bin/gmap_uncompress
9	bin/gmap_process
10	bin/gmap_setup
11	bin/md_coords	27	bin/md_coords
12	bin/fa_coords	28	bin/psl_genes
		29	bin/psl_introns
		30	bin/psl_splicesites
		31	bin/sam_sort
		32	bin/snpindex
		33	bin/uniqscan
		34	bin/uniqscanl
		35	bin/vcf_iit

Return to bug 203334

Lines 2-17 Link Here

(-)Makefile (-3 / +19 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= gmap	4	PORTNAME= gmap
5	PORTVERSION= 2006.04.21	5	PORTVERSION= 2015.09.21
6	PORTREVISION= 1
7	CATEGORIES= biology	6	CATEGORIES= biology
8	MASTER_SITES= http://research-pub.gene.com/gmap/src/	7	MASTER_SITES= http://research-pub.gene.com/gmap/src/
9	DISTNAME= ${PORTNAME}-${PORTVERSION:C\|\.\|-\|g}	8	DISTNAME= ${PORTNAME}-gsnap-${PORTVERSION:C\|\.\|-\|g}
10		9
11	MAINTAINER= rpz@cse.wustl.edu	10	MAINTAINER= rpz@cse.wustl.edu
12	COMMENT= Genomic Mapping and Alignment Program for mRNA and EST Sequences	11	COMMENT= Genomic Mapping and Alignment Program for mRNA and EST Sequences
13		12
		13	LICENSE= GMAP
		14	LICENSE_NAME= GMAP License
		15	LICENSE_FILE= ${WRKSRC}/COPYING
		16	LICENSE_PERMS= dist-mirror pkg-mirror auto-accept
		17
14	USES= gmake perl5	18	USES= gmake perl5
15	GNU_CONFIGURE= yes	19	GNU_CONFIGURE= yes
16		20
		21	WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION:C\|\.\|-\|g}
		22
		23	OPTIONS_DEFINE= SIMD
		24
		25	SIMD_CONFIGURE_OFF= --disable-builtin-popcount --disable-simd
		26
		27	# shebang_fix operates during patch.
		28	# These scripts are created during configure.
		29	post-configure:
		30	${REINPLACE_CMD} -e 's\|/usr/bin/perl\|${PERL}\|g' \
		31	${WRKSRC}/Makefile ${WRKSRC}/util/*.pl
		32
17	.include <bsd.port.mk>	33	.include <bsd.port.mk>