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Bacon" Date: Tue, 22 Sep 2020 00:55:39 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r549546 - head/biology/gmap X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: head/biology/gmap X-SVN-Commit-Revision: 549546 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 22 Sep 2020 00:55:40 -0000 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 - -# 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 +.include 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