Date: Sat, 2 Mar 2013 14:50:25 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r313250 - head/biology/wise Message-ID: <201303021450.r22EoQ1R023075@svn.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: miwi Date: Sat Mar 2 14:50:25 2013 New Revision: 313250 URL: http://svnweb.freebsd.org/changeset/ports/313250 Log: - Update to 2.4.1 PR: 176552 Submitted by: Ports Fury Deleted: head/biology/wise/pkg-plist Modified: head/biology/wise/Makefile (contents, props changed) head/biology/wise/distinfo (contents, props changed) Modified: head/biology/wise/Makefile ============================================================================== --- head/biology/wise/Makefile Sat Mar 2 14:49:28 2013 (r313249) +++ head/biology/wise/Makefile Sat Mar 2 14:50:25 2013 (r313250) @@ -1,24 +1,30 @@ -# New ports collection makefile for: wise -# Date created: 26 February 2002 -# Whom: Tony Maher <tonym@biolateral.com.au> -# +# Created by: Tony Maher <tonym@biolateral.com.au> # $FreeBSD$ -# PORTNAME= wise -PORTVERSION= 2.2.0 +PORTVERSION= 2.4.1 CATEGORIES= biology -MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/ +MASTER_SITES= http://www.ebi.ac.uk/~birney/wise2/ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Intelligent algorithms for DNA searches -WRKTOP= ${WRKDIR}/${DISTNAME} -WRKSRC= ${WRKTOP}/src +OPTIONS_DEFINE= DOCS EXAMPLES + +BUILD_WRKSRC= ${WRKSRC}/src + +USE_GNOME= glib20 MAKEFILE= makefile +MAKE_JOBS_SAFE= yes + SUB_FILES= pkg-message +PORTDOCS= * +PORTEXAMPLES= * +PLIST_FILES= ${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,} +PLIST_DIRS= %%DATADIR%% + # # Actually want an 'ALL_TARGET = all perl' which then requires # 'USE_PERL5= yes' but the perl sub-build is currently broken. @@ -29,68 +35,44 @@ SUB_FILES= pkg-message # something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install' # -BINFILES= dba dnal estwise estwisedb genewise genewisedb \ - genomewise psw pswdb -DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \ - aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \ - gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \ - gon350.bla human.gf human.gp human.stats idenity.bla \ - methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf -DOCFILES= README apiend.tex appendix.tex dynamite.tex \ - genewise21.eps genewise6.eps gettex.pl makefile \ - wise2.tex wise2api.tex wise3arch.tex -EXFILES= README db.hmm hn_est.fa human.genomic \ - keratin_intron.human keratin_intron.mouse pep.fa \ - road.pep rrm.HMM vav.dna xeno.cdna xeno.pep - -# -# Top level makefile does not respect CFLAGS. Fixing it means -# having to fix some of the sub-directory makefiles. -# Note: some makefiles are ok and know that '-c' does not belong -# in CFLAGS and are part of the rule. -# - -post-configure: - @${REINPLACE_CMD} \ - -e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \ - -e s'#\tcsh welcome.csh##;' \ - ${WRKSRC}/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#CFLAGS) $?#CFLAGS) -c $?#;' \ - ${WRKSRC}/base/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ - ${WRKSRC}/dynlibsrc/${MAKEFILE} - @${REINPLACE_CMD} \ - -e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \ - -e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \ - -e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \ - -e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \ - -e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \ - -e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \ - ${WRKSRC}/models/${MAKEFILE} +BINFILES= dba dnal estwise estwisedb genewise genewisedb promoterwise \ + psw pswdb scanwise scanwise_server +DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \ + cb.tmf codon.table gene.stat gon120.bla gon160.bla \ + gon200.bla gon250.bla gon350.bla human.gf human.gp \ + human.stats idenity.bla methods pb.gf pombe.gf tm.pri \ + wise.2 wise.per worm.gf + +.include <bsd.port.options.mk> + +post-patch: + @${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \ + ${REINPLACE_CMD} -e \ + 's|^CC =|CC ?=| ; \ + s|^CFLAGS =|CFLAGS +=| ; \ + s|-O[0-9] | | ; \ + s|-g | | ; \ + s|-g[0-9] | | ; \ + s|-lpthread|-pthread| ; \ + s|glib-config|pkg-config glib-2.0| ; \ + /welcome.csh/s|^|#|' do-install: -.for file in ${BINFILES} - @${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin +.for i in ${BINFILES} + (cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin) .endfor @${MKDIR} ${DATADIR} -.for file in ${DATAFILES} - @${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR} +.for i in ${DATAFILES} + (cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR}) .endfor -.if !defined(NOPORTDOCS) +.if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} -.for file in ${DOCFILES} - @${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR} -.endfor + @(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR}) +.endif +.if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${EXAMPLESDIR} -.for file in ${EXFILES} - @${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR} -.endfor - + @(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR}) .endif - -post-install: @${CAT} ${PKGMESSAGE} .include <bsd.port.mk> Modified: head/biology/wise/distinfo ============================================================================== --- head/biology/wise/distinfo Sat Mar 2 14:49:28 2013 (r313249) +++ head/biology/wise/distinfo Sat Mar 2 14:50:25 2013 (r313250) @@ -1,2 +1,2 @@ -SHA256 (wise2.2.0.tar.gz) = 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780 -SIZE (wise2.2.0.tar.gz) = 2108151 +SHA256 (wise2.4.1.tar.gz) = 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1 +SIZE (wise2.4.1.tar.gz) = 3193910
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201303021450.r22EoQ1R023075>