Date: Tue, 27 Oct 2015 18:49:48 +0000 (UTC) From: Guido Falsi <madpilot@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r400336 - in head/biology/gmap: . files Message-ID: <201510271849.t9RInmMC020519@repo.freebsd.org>
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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@cse.wustl.edu +MAINTAINER= jwbacon@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
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