aboutsummaryrefslogtreecommitdiffstats
path: root/biology/wise/Makefile
blob: 2c99524ff8c96dea505391687f3f7682b7a3fbba (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
# 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

WRKTOP=     ${WRKDIR}/${DISTNAME}
WRKSRC=     ${WRKTOP}/src
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:
    @${PERL} -pi.orig \
        -e s'#^CFLAGS = -c -O#CFLAGS ?= -c -O#;' \
        -e s'#\tcsh welcome.csh##;' \
        ${WRKSRC}/${MAKEFILE}
    @${PERL} -pi.orig \
        -e s'#CFLAGS\) $?#CFLAGS\) -c $?#;' \
        ${WRKSRC}/base/${MAKEFILE}
    @${PERL} -pi.orig \
        -e s'#INCFLAGS\) $?#INCFLAGS\) -c $?#;' \
        ${WRKSRC}/dynlibsrc/${MAKEFILE}
    @${PERL} -pi.orig \
        -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>