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authorMartin Wilke <miwi@FreeBSD.org>2013-03-02 14:50:25 +0000
committerMartin Wilke <miwi@FreeBSD.org>2013-03-02 14:50:25 +0000
commitac8c5f4481e6e1063ab1a69a50eeb28926f32244 (patch)
treed854de0aa815976fd6d402702eafdd5f67993eff /biology/wise
parent47b30b002377cdb9c0b872d3d95317707a8438ef (diff)
downloadports-ac8c5f4481e6e1063ab1a69a50eeb28926f32244.tar.gz
ports-ac8c5f4481e6e1063ab1a69a50eeb28926f32244.zip
Notes
Diffstat (limited to 'biology/wise')
-rw-r--r--biology/wise/Makefile104
-rw-r--r--biology/wise/distinfo4
-rw-r--r--biology/wise/pkg-plist61
3 files changed, 45 insertions, 124 deletions
diff --git a/biology/wise/Makefile b/biology/wise/Makefile
index c7c1e5980911..51286f6a5ffb 100644
--- a/biology/wise/Makefile
+++ b/biology/wise/Makefile
@@ -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; ${MAKE} install'
#
-BINFILES= dba dnal estwise estwisedb genewise genewisedb \
- genomewise psw pswdb
-DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla \
- aa.rnd blosum30.bla blosum62.bla cb.tmf codon.table \
- gene.stat gon120.bla gon160.bla gon200.bla gon250.bla \
- gon350.bla human.gf human.gp human.stats idenity.bla \
- methods pb.gf pombe.gf tm.pri wise.2 wise.per worm.gf
-DOCFILES= README apiend.tex appendix.tex dynamite.tex \
- genewise21.eps genewise6.eps gettex.pl makefile \
- wise2.tex wise2api.tex wise3arch.tex
-EXFILES= README db.hmm hn_est.fa human.genomic \
- keratin_intron.human keratin_intron.mouse pep.fa \
- road.pep rrm.HMM vav.dna xeno.cdna xeno.pep
+BINFILES= dba dnal estwise estwisedb genewise genewisedb promoterwise \
+ psw pswdb scanwise scanwise_server
+DATAFILES= BLOSUM30.bla BLOSUM45.bla BLOSUM62.bla BLOSUM80.bla aa.rnd \
+ cb.tmf codon.table gene.stat gon120.bla gon160.bla \
+ gon200.bla gon250.bla gon350.bla human.gf human.gp \
+ human.stats idenity.bla methods pb.gf pombe.gf tm.pri \
+ wise.2 wise.per worm.gf
-#
-# Top level makefile does not respect CFLAGS. Fixing it means
-# having to fix some of the sub-directory makefiles.
-# Note: some makefiles are ok and know that '-c' does not belong
-# in CFLAGS and are part of the rule.
-#
+.include <bsd.port.options.mk>
-post-configure:
- @${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}
+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>
diff --git a/biology/wise/distinfo b/biology/wise/distinfo
index fe858b076412..1475013ba9c1 100644
--- a/biology/wise/distinfo
+++ b/biology/wise/distinfo
@@ -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
diff --git a/biology/wise/pkg-plist b/biology/wise/pkg-plist
deleted file mode 100644
index 54dc2741b1a5..000000000000
--- a/biology/wise/pkg-plist
+++ /dev/null
@@ -1,61 +0,0 @@
-bin/genomewise
-%%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%DOCSDIR%%/apiend.tex
-%%PORTDOCS%%%%DOCSDIR%%/appendix.tex
-%%PORTDOCS%%%%DOCSDIR%%/dynamite.tex
-%%PORTDOCS%%%%DOCSDIR%%/genewise21.eps
-%%PORTDOCS%%%%DOCSDIR%%/genewise6.eps
-%%PORTDOCS%%%%DOCSDIR%%/gettex.pl
-%%PORTDOCS%%%%DOCSDIR%%/makefile
-%%PORTDOCS%%%%DOCSDIR%%/wise2.tex
-%%PORTDOCS%%%%DOCSDIR%%/wise2api.tex
-%%PORTDOCS%%%%DOCSDIR%%/wise3arch.tex
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hn_est.fa
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/human.genomic
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.human
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/keratin_intron.mouse
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pep.fa
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/road.pep
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rrm.HMM
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/vav.dna
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.cdna
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/xeno.pep
-%%DATADIR%%/BLOSUM30.bla
-%%DATADIR%%/BLOSUM45.bla
-%%DATADIR%%/BLOSUM62.bla
-%%DATADIR%%/BLOSUM80.bla
-%%DATADIR%%/aa.rnd
-%%DATADIR%%/blosum30.bla
-%%DATADIR%%/blosum62.bla
-%%DATADIR%%/cb.tmf
-%%DATADIR%%/codon.table
-%%DATADIR%%/gene.stat
-%%DATADIR%%/gon120.bla
-%%DATADIR%%/gon160.bla
-%%DATADIR%%/gon200.bla
-%%DATADIR%%/gon250.bla
-%%DATADIR%%/gon350.bla
-%%DATADIR%%/human.gf
-%%DATADIR%%/human.gp
-%%DATADIR%%/human.stats
-%%DATADIR%%/idenity.bla
-%%DATADIR%%/methods
-%%DATADIR%%/pb.gf
-%%DATADIR%%/pombe.gf
-%%DATADIR%%/tm.pri
-%%DATADIR%%/wise.2
-%%DATADIR%%/wise.per
-%%DATADIR%%/worm.gf
-bin/dba
-bin/dnal
-bin/estwise
-bin/estwisedb
-bin/genewise
-bin/genewisedb
-bin/psw
-bin/pswdb
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
-@dirrm %%DATADIR%%