svn commit: r400336 - in head/biology/gmap: . files

[Guido Falsi]

Author: madpilot
Date: Tue Oct 27 18:49:48 2015
New Revision: 400336
URL: https://svnweb.freebsd.org/changeset/ports/400336

Log:
  - Update to 2015.09.21
  - Add License
  - Add SIMD option disabled by default to avoid creating official
    packags with CPU specific optimizations
  - Add pkg-message explaining how to get an optimized binary
  - Assign maintainership to submitter
  
  PR:		203334
  Submitted by:	jwbacon at tds.net
  Approved by:	Maintainer timeout

Added:
  head/biology/gmap/pkg-message   (contents, props changed)
Deleted:
  head/biology/gmap/files/
Modified:
  head/biology/gmap/Makefile
  head/biology/gmap/distinfo
  head/biology/gmap/pkg-plist

Modified: head/biology/gmap/Makefile
==============================================================================
--- head/biology/gmap/Makefile	Tue Oct 27 18:48:55 2015	(r400335)
+++ head/biology/gmap/Makefile	Tue Oct 27 18:49:48 2015	(r400336)
@@ -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 at cse.wustl.edu
+MAINTAINER=	jwbacon at 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>

Modified: head/biology/gmap/distinfo
==============================================================================
--- head/biology/gmap/distinfo	Tue Oct 27 18:48:55 2015	(r400335)
+++ head/biology/gmap/distinfo	Tue Oct 27 18:49:48 2015	(r400336)
@@ -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

Added: head/biology/gmap/pkg-message
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/gmap/pkg-message	Tue Oct 27 18:49:48 2015	(r400336)
@@ -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.

Modified: head/biology/gmap/pkg-plist
==============================================================================
--- head/biology/gmap/pkg-plist	Tue Oct 27 18:48:55 2015	(r400335)
+++ head/biology/gmap/pkg-plist	Tue Oct 27 18:49:48 2015	(r400336)
@@ -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