diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2020-09-22 00:55:39 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2020-09-22 00:55:39 +0000 |
| commit | 12d8a81d519b773277430ca1e4677b3aef2b54eb (patch) | |
| tree | b1b8d7b9c808d24701984e46c44c37a88a1e5669 /biology | |
| parent | 0cfe5d5a5bfad6366000a366eb7dbb9033aed651 (diff) | |
| download | ports-12d8a81d519b773277430ca1e4677b3aef2b54eb.tar.gz ports-12d8a81d519b773277430ca1e4677b3aef2b54eb.zip | |
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
Notes
Notes:
svn path=/head/; revision=549546
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/gmap/Makefile | 25 | ||||
| -rw-r--r-- | biology/gmap/distinfo | 5 | ||||
| -rw-r--r-- | biology/gmap/pkg-plist | 14 |
3 files changed, 17 insertions, 27 deletions
diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile index 12e05ad91490..4116e38b271a 100644 --- a/biology/gmap/Makefile +++ b/biology/gmap/Makefile @@ -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> diff --git a/biology/gmap/distinfo b/biology/gmap/distinfo index 07ef00669c29..9ed16c632335 100644 --- a/biology/gmap/distinfo +++ b/biology/gmap/distinfo @@ -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 diff --git a/biology/gmap/pkg-plist b/biology/gmap/pkg-plist index ec7d83f2035a..65b5bd55c23b 100644 --- a/biology/gmap/pkg-plist +++ b/biology/gmap/pkg-plist @@ -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 |