blob: 2a1fd99762dedac254e0cf3f3e1650afc27cb298 (
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
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
|
# New ports collection makefile for: p5-bioperl-devel
# Date created: 13 August 2001
# Whom: Johann Visagie <wjv@FreeBSD.org>
#
# $FreeBSD$
#
PORTNAME= bioperl
PORTVERSION= 0.9.0
CATEGORIES= biology perl5
MASTER_SITES= ftp://bioperl.org/pub/DIST/ \
http://bioperl.org/Core/Latest/
PKGNAMEPREFIX= p5-
PKGNAMESUFFIX= -devel
DISTFILES= ${DISTNAME}${EXTRACT_SUFX}
MAINTAINER= wjv@FreeBSD.org
# These are all run-time dependencies, but listing them in ${BUILD_DEPENDS}
# prevents a flood of build-time warnings.
BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Node.pm:${PORTSDIR}/textproc/p5-XML-Node \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \
${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer
RUN_DEPENDS= ${BUILD_DEPENDS}
PERL_CONFIGURE= YES
.if defined(WITH_CORBA)
WITH_CORBA_CLIENT= YES
WITH_CORBA_SERVER= YES
.endif
EXT_VERSION= 0.6
CORBA_CLIENT_VERSION= 0.2
CORBA_SERVER_VERSION= 0.2
GUI_VERSION= 0.7
DISTFILES+= bioperl-ext-${EXT_VERSION}${EXTRACT_SUFX}
EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06/Bio/Ext/Align
.if defined(WITH_CORBA_CLIENT)
BUILD_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_CORBA_SERVER)
BUILD_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
RUN_DEPENDS+= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/CORBA/ORBit.pm:${PORTSDIR}/devel/p5-ORBit
.endif
.if defined(WITH_GUI)
RUN_DEPENDS+= ptksh:${PORTSDIR}/x11-toolkits/p5-Tk
.endif
.for ext in CORBA_CLIENT CORBA_SERVER GUI
.if defined(WITH_${ext})
EXTLIST+= ${ext}
DISTFILES+= bioperl-${ext:L:S/_/-/}-${${ext}_VERSION}${EXTRACT_SUFX}
${ext}_WRKSRC= ${WRKDIR}/bioperl-${ext:L:S/_/-/}
PLIST_${ext}= ""
.else
PLIST_${ext}= "@comment "
.endif
PLIST_SUB+= PLIST_${ext}=${PLIST_${ext}}
.endfor
MAN3= Bio::AlignIO.3 Bio::AlignIO::bl2seq.3 \
Bio::AlignIO::clustalw.3 Bio::AlignIO::fasta.3 \
Bio::AlignIO::mase.3 Bio::AlignIO::meme.3 Bio::AlignIO::msf.3 \
Bio::AlignIO::nexus.3 Bio::AlignIO::pfam.3 \
Bio::AlignIO::phylip.3 Bio::AlignIO::prodom.3 \
Bio::AlignIO::selex.3 Bio::AlignIO::stockholm.3 \
Bio::Annotation.3 Bio::Annotation::Comment.3 \
Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \
Bio::DB::Ace.3 Bio::DB::EMBL.3 Bio::DB::Fasta.3 \
Bio::DB::GDB.3 Bio::DB::GFF.3 Bio::DB::GFF::Adaptor::dbi.3 \
Bio::DB::GFF::Aggregator.3 \
Bio::DB::GFF::Aggregator::alignment.3 \
Bio::DB::GFF::Aggregator::clone.3 \
Bio::DB::GFF::Aggregator::none.3 \
Bio::DB::GFF::Aggregator::transcript.3 \
Bio::DB::GFF::Featname.3 Bio::DB::GFF::Feature.3 \
Bio::DB::GFF::Homol.3 Bio::DB::GFF::RelSegment.3 \
Bio::DB::GFF::Segment.3 Bio::DB::GFF::Typename.3 \
Bio::DB::GenBank.3 Bio::DB::GenPept.3 Bio::DB::NCBIHelper.3 \
Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 Bio::DB::SwissProt.3 \
Bio::DB::Universal.3 Bio::DB::UpdateableSeqI.3 \
Bio::DB::WebDBSeqI.3 Bio::DBLinkContainerI.3 \
Bio::Factory::ApplicationFactoryI.3 \
Bio::Factory::DriverFactory.3 Bio::Factory::EMBOSS.3 \
Bio::Factory::SeqAnalysisParserFactory.3 \
Bio::Factory::SeqAnalysisParserFactoryI.3 \
Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \
Bio::Index::EMBL.3 Bio::Index::Fasta.3 Bio::Index::GenBank.3 \
Bio::Index::SwissPfam.3 Bio::Index::Swissprot.3 \
Bio::LiveSeq::AARange.3 Bio::LiveSeq::Chain.3 \
Bio::LiveSeq::ChainI.3 Bio::LiveSeq::DNA.3 \
Bio::LiveSeq::Exon.3 Bio::LiveSeq::Gene.3 \
Bio::LiveSeq::IO::BioPerl.3 Bio::LiveSeq::IO::Loader.3 \
Bio::LiveSeq::IO::SRS.3 Bio::LiveSeq::Intron.3 \
Bio::LiveSeq::Mutation.3 Bio::LiveSeq::Mutator.3 \
Bio::LiveSeq::Prim_Transcript.3 Bio::LiveSeq::Range.3 \
Bio::LiveSeq::Repeat_Region.3 Bio::LiveSeq::Repeat_Unit.3 \
Bio::LiveSeq::SeqI.3 Bio::LiveSeq::Transcript.3 \
Bio::LiveSeq::Translation.3 Bio::LocatableSeq.3 \
Bio::Location::AvWithinCoordPolicy.3 \
Bio::Location::CoordinatePolicyI.3 Bio::Location::Fuzzy.3 \
Bio::Location::FuzzyLocationI.3 \
Bio::Location::NarrowestCoordPolicy.3 Bio::Location::Simple.3 \
Bio::Location::Split.3 Bio::Location::SplitLocationI.3 \
Bio::Location::WidestCoordPolicy.3 Bio::LocationI.3 \
Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \
Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \
Bio::Root::IO.3 Bio::Root::IOManager.3 Bio::Root::Object.3 \
Bio::Root::RootI.3 Bio::Root::Utilities.3 Bio::Root::Vector.3 \
Bio::Root::Xref.3 Bio::SearchDist.3 Bio::Seq.3 \
Bio::Seq::LargePrimarySeq.3 Bio::Seq::LargeSeq.3 \
Bio::Seq::RichSeq.3 Bio::Seq::RichSeqI.3 \
Bio::SeqAnalysisParserI.3 Bio::SeqFeature::Computation.3 \
Bio::SeqFeature::Exon.3 Bio::SeqFeature::FeaturePair.3 \
Bio::SeqFeature::Gene::Exon.3 Bio::SeqFeature::Gene::ExonI.3 \
Bio::SeqFeature::Gene::GeneStructure.3 \
Bio::SeqFeature::Gene::GeneStructureI.3 \
Bio::SeqFeature::Gene::Transcript.3 \
Bio::SeqFeature::Gene::TranscriptI.3 \
Bio::SeqFeature::Generic.3 Bio::SeqFeature::Intron.3 \
Bio::SeqFeature::PolyA.3 Bio::SeqFeature::Promoter.3 \
Bio::SeqFeature::Similarity.3 \
Bio::SeqFeature::SimilarityPair.3 Bio::SeqFeature::UTR3.3 \
Bio::SeqFeature::UTR5.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \
Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 Bio::SeqIO::MultiFile.3 \
Bio::SeqIO::ace.3 Bio::SeqIO::embl.3 Bio::SeqIO::fasta.3 \
Bio::SeqIO::game.3 Bio::SeqIO::game::featureHandler.3 \
Bio::SeqIO::game::idHandler.3 Bio::SeqIO::game::seqHandler.3 \
Bio::SeqIO::gcg.3 Bio::SeqIO::genbank.3 \
Bio::SeqIO::largefasta.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \
Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SeqUtils.3 \
Bio::SimpleAlign.3 Bio::Species.3 Bio::Tools::AlignFactory.3 \
Bio::Tools::AnalysisResult.3 Bio::Tools::BPbl2seq.3 \
Bio::Tools::BPlite.3 Bio::Tools::BPlite::Iteration.3 \
Bio::Tools::BPpsilite.3 Bio::Tools::Blast.3 \
Bio::Tools::Blast::HSP.3 Bio::Tools::Blast::HTML.3 \
Bio::Tools::Blast::Run::LocalBlast.3 \
Bio::Tools::Blast::Run::Webblast.3 Bio::Tools::Blast::Sbjct.3 \
Bio::Tools::CodonTable.3 Bio::Tools::EPCR.3 \
Bio::Tools::ESTScan.3 Bio::Tools::Fasta.3 Bio::Tools::GFF.3 \
Bio::Tools::Genemark.3 Bio::Tools::Genscan.3 \
Bio::Tools::Grail.3 Bio::Tools::HMMER::Domain.3 \
Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \
Bio::Tools::IUPAC.3 Bio::Tools::MZEF.3 Bio::Tools::OddCodes.3 \
Bio::Tools::Prediction::Exon.3 Bio::Tools::Prediction::Gene.3 \
Bio::Tools::RestrictionEnzyme.3 \
Bio::Tools::Run::Alignment::Clustalw.3 \
Bio::Tools::Run::Alignment::TCoffee.3 \
Bio::Tools::Run::EMBOSSApplication.3 \
Bio::Tools::Run::RemoteBlast.3 \
Bio::Tools::Run::StandAloneBlast.3 Bio::Tools::SeqAnal.3 \
Bio::Tools::SeqPattern.3 Bio::Tools::SeqStats.3 \
Bio::Tools::SeqWords.3 Bio::Tools::Sigcleave.3 \
Bio::Tools::Sim4::Exon.3 Bio::Tools::Sim4::Results.3 \
Bio::Tools::WWW.3 Bio::Tools::pSW.3 Bio::UnivAln.3 \
Bio::Variation::AAChange.3 Bio::Variation::AAReverseMutate.3 \
Bio::Variation::Allele.3 Bio::Variation::DNAMutation.3 \
Bio::Variation::IO.3 Bio::Variation::IO::flat.3 \
Bio::Variation::IO::xml.3 Bio::Variation::RNAChange.3 \
Bio::Variation::SeqDiff.3 Bio::Variation::VariantI.3 \
bioback.3 biodesign.3 bioperl.3 biostart.3 bptutorial.3
.if defined(WITH_CORBA_CLIENT)
MAN3+= Bio::CorbaClient::PrimarySeq.3 Bio::CorbaClient::Seq.3 \
Bio::CorbaClient::SeqFeature.3 Bio::CorbaClient::Base.3 \
Bio::SeqIO::biocorba.3 Bio::DB::Biocorba.3 \
Bio::CorbaClient::Client.3 Bio::CorbaClient::ORB.3
.endif
.if defined(WITH_CORBA_SERVER)
MAN3+= Bio::CorbaServer::BioEnv.3 Bio::CorbaServer::AnonymousSeq.3 \
Bio::CorbaServer::PrimarySeq.3 Bio::CorbaServer::SeqFeature.3 \
Bio::CorbaServer::PrimarySeqDB.3 \
Bio::CorbaServer::PrimarySeqIterator.3 \
Bio::CorbaServer::PrimarySeqVector.3 \
Bio::CorbaServer::Seq.3 \
Bio::CorbaServer::SeqDB.3 Bio::CorbaServer::Base.3 \
Bio::CorbaServer::SeqFeatureIterator.3 \
Bio::CorbaServer::SeqFeatureVector.3 \
Bio::CorbaServer::Server.3
.endif
.if defined(WITH_GUI)
MAN3+= Bio::Tk::HitDisplay.3 Bio::Tk::SeqCanvas.3
.endif
MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION}
pre-fetch:
.if !defined(BATCH) && (!defined(WITH_CORBA_CLIENT) || \
!defined(WITH_CORBA_SERVER) || !defined(WITH_GUI))
@ ${CAT} ${FILESDIR}/ext.msg
.endif
post-configure:
@ cd ${EXT_WRKSRC} && \
${SETENV} ${CONFIGURE_ENV} \
${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.for ext in ${EXTLIST}
@ cd ${${ext}_WRKSRC} && \
${PERL5} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
.endfor
post-build:
@ cd ${EXT_WRKSRC} && \
${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
.for ext in ${EXTLIST}
@ cd ${${ext}_WRKSRC} && ${SETENV} ${MAKE_ENV} \
${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}
.endfor
post-install:
@ cd ${EXT_WRKSRC} && \
${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
.for ext in ${EXTLIST}
@ cd ${${ext}_WRKSRC} && \
${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \
${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}
.endfor
.include <bsd.port.mk>
|
