blob: 9b00cae29bc5532a8dd8b7823127483b00747c86 (
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
|
# Created by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
# $FreeBSD$
PORTNAME= velvet
PORTVERSION= 1.1.04
CATEGORIES= biology
MASTER_SITES= http://www.ebi.ac.uk/~zerbino/velvet/
DISTNAME= ${PORTNAME}_${PORTVERSION}
EXTRACT_SUFX= .tgz
MAINTAINER= mzaki@m.u-tokyo.ac.jp
COMMENT= Sequence assembler for very short reads
USE_GMAKE= yes
ALL_TARGET= default
MAXKMERLENGTH?= 31
VELVET_CATEGORIES?= 2
MAKE_ENV+= MAXKMERLENGTH=${MAXKMERLENGTH} CATEGORIES=${VELVET_CATEGORIES}
USES= perl5
USE_PERL5= run
BINARIES= velvetg velveth
SCRIPTS= shuffleSequences_fasta.pl shuffleSequences_fastq.pl \
contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl \
contrib/afg_handling/asmbly_splitter.pl \
contrib/afg_handling/snp_view.pl \
contrib/columbus_scripts/enlarge_exons.pl \
contrib/columbus_scripts/gff2fasta.pl \
contrib/columbus_scripts/merge_gtf_exons.pl \
contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl \
contrib/extractContigReads/extractContigReads.pl \
contrib/fasta2agp/fasta2agp.pl \
contrib/observed-insert-length.pl/observed-insert-length.pl \
contrib/select_paired/select_paired.pl \
contrib/show_repeats/show_repeats.pl
PERLMOD_DIRS= contrib/VelvetOptimiser-2.1.7/VelvetOpt
PERLMOD_FILES= contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm \
contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm \
contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm \
contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm
.if !defined(WITHOUT_PYTHON)
USE_PYTHON= yes
SCRIPTS+= contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
.endif
.for f in ${BINARIES} ${SCRIPTS}
PLIST_FILES+= bin/${f:T}
.endfor
.for d in ${PERLMOD_DIRS}
PLIST_DIRS+= %%SITE_PERL%%/${d:T}
.endfor
.for f in ${PERLMOD_FILES}
PLIST_FILES+= %%SITE_PERL%%/${f:H:T}/${f:T}
.endfor
PORTDOCS= ChangeLog Manual.pdf Columbus_manual.pdf
NO_STAGE= yes
OPTIONS_DEFINE= DOCS
.include <bsd.port.options.mk>
post-patch:
.for f in ${SCRIPTS}
${REINPLACE_CMD} -e s,#!/usr/bin/perl,${PERL}, ${WRKSRC}/${f}
.endfor
.if !defined(WITHOUT_PYTHON)
${REINPLACE_CMD} -e s,#!/usr/bin/python,${PYTHON_CMD}, ${WRKSRC}/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py
.endif
do-install:
.for f in ${BINARIES}
${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
.endfor
.for f in ${SCRIPTS}
${INSTALL_SCRIPT} ${WRKSRC}/${f} ${PREFIX}/bin/${f:T}
.endfor
.for d in ${PERLMOD_DIRS}
${MKDIR} ${PREFIX}/${SITE_PERL_REL}/${d:T}
.endfor
.for f in ${PERLMOD_FILES}
${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/${SITE_PERL_REL}/${f:H:T}/${f:T}
.endfor
.if ${PORT_OPTIONS:MDOCS}
${MKDIR} ${DOCSDIR}
.for f in ${PORTDOCS}
${INSTALL_MAN} ${WRKSRC}/${f} ${DOCSDIR}
.endfor
.endif
.include <bsd.port.mk>
|
