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- Update to 2.4.1
PR: 176552 Submitted by: Ports Fury
This commit is contained in:
Martin Wilke
parent
47b30b0023
commit
ac8c5f4481
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=313250
@ -1,24 +1,30 @@
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# New ports collection makefile for: wise
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# Date created: 26 February 2002
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# Whom: Tony Maher <tonym@biolateral.com.au>
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#
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# Created by: Tony Maher <tonym@biolateral.com.au>
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# $FreeBSD$
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#
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PORTNAME= wise
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PORTVERSION= 2.2.0
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PORTVERSION= 2.4.1
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
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MASTER_SITES= http://www.ebi.ac.uk/~birney/wise2/
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DISTNAME= ${PORTNAME}${PORTVERSION}
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MAINTAINER= ports@FreeBSD.org
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COMMENT= Intelligent algorithms for DNA searches
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WRKTOP= ${WRKDIR}/${DISTNAME}
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WRKSRC= ${WRKTOP}/src
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OPTIONS_DEFINE= DOCS EXAMPLES
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BUILD_WRKSRC= ${WRKSRC}/src
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USE_GNOME= glib20
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MAKEFILE= makefile
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MAKE_JOBS_SAFE= yes
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SUB_FILES= pkg-message
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PORTDOCS= *
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PORTEXAMPLES= *
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PLIST_FILES= ${BINFILES:S,^,bin/,} ${DATAFILES:S,^,%%DATADIR%%/,}
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PLIST_DIRS= %%DATADIR%%
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#
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# Actually want an 'ALL_TARGET = all perl' which then requires
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# 'USE_PERL5= yes' but the perl sub-build is currently broken.
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@ -29,68 +35,44 @@ SUB_FILES= pkg-message
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# something like '@cd ${WRKSRC}/perl/Wise2; ${MAKE} install'
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#
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BINFILES= dba dnal estwise estwisedb genewise genewisedb \
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genomewise psw pswdb
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DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \
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aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \
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gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \
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gon350.bla human.gf human.gp human.stats idenity.bla \
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methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf
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DOCFILES= README apiend.tex appendix.tex dynamite.tex \
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genewise21.eps genewise6.eps gettex.pl makefile \
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wise2.tex wise2api.tex wise3arch.tex
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EXFILES= README db.hmm hn_est.fa human.genomic \
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keratin_intron.human keratin_intron.mouse pep.fa \
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road.pep rrm.HMM vav.dna xeno.cdna xeno.pep
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BINFILES= dba dnal estwise estwisedb genewise genewisedb promoterwise \
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psw pswdb scanwise scanwise_server
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DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \
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cb.tmf codon.table gene.stat gon120.bla gon160.bla \
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gon200.bla gon250.bla gon350.bla human.gf human.gp \
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human.stats idenity.bla methods pb.gf pombe.gf tm.pri \
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wise.2 wise.per worm.gf
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#
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# Top level makefile does not respect CFLAGS. Fixing it means
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# having to fix some of the sub-directory makefiles.
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# Note: some makefiles are ok and know that '-c' does not belong
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# in CFLAGS and are part of the rule.
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#
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.include <bsd.port.options.mk>
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post-configure:
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@${REINPLACE_CMD} \
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-e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \
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-e s'#\tcsh welcome.csh##;' \
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${WRKSRC}/${MAKEFILE}
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@${REINPLACE_CMD} \
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-e s'#CFLAGS) $?#CFLAGS) -c $?#;' \
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${WRKSRC}/base/${MAKEFILE}
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@${REINPLACE_CMD} \
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-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
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${WRKSRC}/dynlibsrc/${MAKEFILE}
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@${REINPLACE_CMD} \
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-e s'#INCFLAGS) $?#INCFLAGS) -c $?#;' \
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-e s'#CFLAGS) estwise.c#CFLAGS) -c estwise.c#;' \
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-e s'#CFLAGS) estwiseb.c#CFLAGS) -c estwiseb.c#;' \
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-e s'#CFLAGS) estwisedb.c#CFLAGS) -c estwisedb.c#;' \
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-e s'#CFLAGS) genewise.c#CFLAGS) -c genewise.c#;' \
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-e s'#CFLAGS) genewisedb.c#CFLAGS) -c genewisedb.c#;' \
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${WRKSRC}/models/${MAKEFILE}
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post-patch:
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@${FIND} ${BUILD_WRKSRC} -name "makefile" | ${XARGS} \
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${REINPLACE_CMD} -e \
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's|^CC =|CC ?=| ; \
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s|^CFLAGS =|CFLAGS +=| ; \
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s|-O[0-9] | | ; \
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s|-g | | ; \
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s|-g[0-9] | | ; \
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s|-lpthread|-pthread| ; \
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s|glib-config|pkg-config glib-2.0| ; \
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/welcome.csh/s|^|#|'
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do-install:
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.for file in ${BINFILES}
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@${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin
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.for i in ${BINFILES}
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(cd ${BUILD_WRKSRC}/bin && ${INSTALL_PROGRAM} ${i} ${PREFIX}/bin)
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.endfor
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@${MKDIR} ${DATADIR}
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.for file in ${DATAFILES}
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@${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR}
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.for i in ${DATAFILES}
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(cd ${WRKSRC}/wisecfg && ${INSTALL_DATA} ${i} ${DATADIR})
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.endfor
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.if !defined(NOPORTDOCS)
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.if ${PORT_OPTIONS:MDOCS}
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@${MKDIR} ${DOCSDIR}
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.for file in ${DOCFILES}
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@${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR}
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.endfor
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@${MKDIR} ${EXAMPLESDIR}
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.for file in ${EXFILES}
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@${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR}
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.endfor
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@(cd ${WRKSRC}/docs && ${COPYTREE_SHARE} . ${DOCSDIR})
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.endif
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.if ${PORT_OPTIONS:MEXAMPLES}
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@${MKDIR} ${EXAMPLESDIR}
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@(cd ${WRKSRC}/test_data && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
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.endif
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post-install:
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@${CAT} ${PKGMESSAGE}
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.include <bsd.port.mk>
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@ -1,2 +1,2 @@
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SHA256 (wise2.2.0.tar.gz) = 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
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SIZE (wise2.2.0.tar.gz) = 2108151
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SHA256 (wise2.4.1.tar.gz) = 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1
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SIZE (wise2.4.1.tar.gz) = 3193910
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@ -1,61 +0,0 @@
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bin/genomewise
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%%PORTDOCS%%%%DOCSDIR%%/README
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%%PORTDOCS%%%%DOCSDIR%%/apiend.tex
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%%PORTDOCS%%%%DOCSDIR%%/appendix.tex
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%%PORTDOCS%%%%DOCSDIR%%/dynamite.tex
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%%PORTDOCS%%%%DOCSDIR%%/genewise21.eps
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%%PORTDOCS%%%%DOCSDIR%%/genewise6.eps
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%%PORTDOCS%%%%DOCSDIR%%/gettex.pl
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%%PORTDOCS%%%%DOCSDIR%%/makefile
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%%PORTDOCS%%%%DOCSDIR%%/wise2.tex
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%%PORTDOCS%%%%DOCSDIR%%/wise2api.tex
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%%PORTDOCS%%%%DOCSDIR%%/wise3arch.tex
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db.hmm
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hn_est.fa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/human.genomic
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.human
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.mouse
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pep.fa
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/road.pep
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rrm.HMM
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vav.dna
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.cdna
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.pep
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%%DATADIR%%/BLOSUM30.bla
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%%DATADIR%%/BLOSUM45.bla
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%%DATADIR%%/BLOSUM62.bla
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%%DATADIR%%/BLOSUM80.bla
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%%DATADIR%%/aa.rnd
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%%DATADIR%%/blosum30.bla
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%%DATADIR%%/blosum62.bla
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%%DATADIR%%/cb.tmf
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%%DATADIR%%/codon.table
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%%DATADIR%%/gene.stat
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%%DATADIR%%/gon120.bla
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%%DATADIR%%/gon160.bla
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%%DATADIR%%/gon200.bla
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%%DATADIR%%/gon250.bla
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%%DATADIR%%/gon350.bla
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%%DATADIR%%/human.gf
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%%DATADIR%%/human.gp
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%%DATADIR%%/human.stats
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%%DATADIR%%/idenity.bla
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%%DATADIR%%/methods
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%%DATADIR%%/pb.gf
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%%DATADIR%%/pombe.gf
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%%DATADIR%%/tm.pri
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%%DATADIR%%/wise.2
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%%DATADIR%%/wise.per
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%%DATADIR%%/worm.gf
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bin/dba
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bin/dnal
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bin/estwise
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bin/estwisedb
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bin/genewise
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bin/genewisedb
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bin/psw
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bin/pswdb
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%%PORTDOCS%%@dirrm %%DOCSDIR%%
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%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
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@dirrm %%DATADIR%%
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