blob: 426eb7c161ff86d1d310b9acecbe0e6f6517cbd6 (
plain) (
blame)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
|
# New ports collection makefile for: wise
# Date created: 26 February 2002
# Whom: Tony Maher <tonym@biolateral.com.au>
#
# $FreeBSD$
#
PORTNAME= wise
PORTVERSION= 2.2.0
CATEGORIES= biology
MASTER_SITES= ftp://ftp.sanger.ac.uk/pub/birney/wise2/
DISTNAME= ${PORTNAME}${PORTVERSION}
MAINTAINER= tonym@biolateral.com.au
COMMENT= Intelligent algorithms for DNA searches
WRKTOP= ${WRKDIR}/${DISTNAME}
WRKSRC= ${WRKTOP}/src
USE_REINPLACE= yes
MAKEFILE= makefile
#
# Actually want an 'ALL_TARGET = all perl' which then requires
# 'USE_PERL5= yes' but the perl sub-build is currently broken.
# The perl stuff is only so you can use the base libraries/functions
# from perl scripts. This is extra, independent functionality for the
# port and not required for the base system which are C applications.
# When the perl part is fixed, it will require an install line
# 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}
do-install:
.for file in ${BINFILES}
@${INSTALL_PROGRAM} ${WRKSRC}/bin/${file} ${PREFIX}/bin
.endfor
@${MKDIR} ${DATADIR}
.for file in ${DATAFILES}
@${INSTALL_DATA} ${WRKTOP}/wisecfg/${file} ${DATADIR}
.endfor
.if !defined(NOPORTDOCS)
@${MKDIR} ${DOCSDIR}
.for file in ${DOCFILES}
@${INSTALL_DATA} ${WRKTOP}/docs/${file} ${DOCSDIR}
.endfor
@${MKDIR} ${EXAMPLESDIR}
.for file in ${EXFILES}
@${INSTALL_DATA} ${WRKTOP}/test_data/${file} ${EXAMPLESDIR}
.endfor
.endif
post-install:
@${SED} -E -e 's#PREFIX#${PREFIX}#' -e '/(^\[|]$$)/d' ${PKGMESSAGE}
.include <bsd.port.mk>
|
