svn commit: r549546 - head/biology/gmap
Jason W. Bacon
jwb at FreeBSD.org
Tue Sep 22 00:55:40 UTC 2020
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
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