svn commit: r549546 - head/biology/gmap

[Jason W. Bacon]

Author: jwb
Date: Tue Sep 22 00:55:39 2020
New Revision: 549546
URL: https://svnweb.freebsd.org/changeset/ports/549546

Log:
  biology/gmap: Upgrade to 2020.09.12
  
  First upgrade in 5 years, so numerous improvements
  Unsure if powerpc is still supported upstream
  Code mentions power8, but does not build on my Mac G5

Modified:
  head/biology/gmap/Makefile
  head/biology/gmap/distinfo
  head/biology/gmap/pkg-plist

Modified: head/biology/gmap/Makefile
==============================================================================
--- head/biology/gmap/Makefile	Tue Sep 22 00:38:06 2020	(r549545)
+++ head/biology/gmap/Makefile	Tue Sep 22 00:55:39 2020	(r549546)
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	gmap
-PORTVERSION=	2015.09.21
+PORTVERSION=	2020.09.12
 CATEGORIES=	biology
 MASTER_SITES=	http://research-pub.gene.com/gmap/src/
 DISTNAME=	${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g}
@@ -15,32 +15,17 @@ LICENSE_NAME=	GMAP License
 LICENSE_FILE=	${WRKSRC}/COPYING
 LICENSE_PERMS=	dist-mirror pkg-mirror auto-accept
 
-BROKEN_aarch64=		invokes x86 assembler
-BROKEN_armv6=		invokes x86 assembler
-BROKEN_armv7=		invokes x86 assembler
-BROKEN_mips64=		invokes x86 assembler
-BROKEN_sparc64=		invokes x86 assembler
+ONLY_FOR_ARCHS=		amd64 i386
+ONLY_FOR_ARCHS_REASON=	Upstream supports only x86 and possibly POWER8
 
 USES=		gmake perl5
 GNU_CONFIGURE=	yes
 
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C|\.|-|g}
+CFLAGS+=	-fcommon
 
 OPTIONS_DEFINE=	SIMD
 
 SIMD_CONFIGURE_OFF=	--disable-builtin-popcount --disable-simd
 
-.include <bsd.port.pre.mk>
-
-# 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
-.if ${ARCH:Mpowerpc*}
-# XXX MCL unknown why this shows up as true.  knowledge of autoconf needed.
-	${REINPLACE_CMD} -e 's|#define HAVE_ASM_BSR 1||' \
-		${WRKSRC}/src/config.h
-.endif
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>

Modified: head/biology/gmap/distinfo
==============================================================================
--- head/biology/gmap/distinfo	Tue Sep 22 00:38:06 2020	(r549545)
+++ head/biology/gmap/distinfo	Tue Sep 22 00:55:39 2020	(r549546)
@@ -1,2 +1,3 @@
-SHA256 (gmap-gsnap-2015-09-21.tar.gz) = af78237ee9b90ba4416872b3509536060749c3622bbcaadec10e2dcc01301d9c
-SIZE (gmap-gsnap-2015-09-21.tar.gz) = 4168019
+TIMESTAMP = 1600434673
+SHA256 (gmap-gsnap-2020-09-12.tar.gz) = 9f267d8d165a99b8cb41a22217ed9f8a987ba8b8f8303b0ae867d3e8bf96cef3
+SIZE (gmap-gsnap-2020-09-12.tar.gz) = 4470731

Modified: head/biology/gmap/pkg-plist
==============================================================================
--- head/biology/gmap/pkg-plist	Tue Sep 22 00:38:06 2020	(r549545)
+++ head/biology/gmap/pkg-plist	Tue Sep 22 00:55:39 2020	(r549546)
@@ -1,5 +1,6 @@
 bin/atoiindex
 bin/cmetindex
+bin/cpuid
 bin/dbsnp_iit
 bin/ensembl_genes
 bin/fa_coords
@@ -8,28 +9,31 @@ bin/gff3_genes
 bin/gff3_introns
 bin/gff3_splicesites
 bin/gmap
+bin/gmap.nosimd
 bin/gmap_build
-bin/gmap_compress
+bin/gmap_cat
 bin/gmap_process
-bin/gmap_reassemble
-bin/gmap_uncompress
 bin/gmapindex
 bin/gmapl
+bin/gmapl.nosimd
 bin/gsnap
+bin/gsnap.nosimd
 bin/gsnapl
+bin/gsnapl.nosimd
 bin/gtf_genes
 bin/gtf_introns
 bin/gtf_splicesites
+bin/gtf_transcript_splicesites
 bin/gvf_iit
 bin/iit_dump
 bin/iit_get
 bin/iit_store
+bin/indexdb_cat
 bin/md_coords
 bin/psl_genes
 bin/psl_introns
 bin/psl_splicesites
 bin/sam_sort
 bin/snpindex
-bin/uniqscan
-bin/uniqscanl
+bin/trindex
 bin/vcf_iit