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mirror of https://git.FreeBSD.org/ports.git synced 2024-11-23 00:43:28 +00:00

LibSBML is an open-source programming library to help you read, write,

manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:		ports/135022
Submitted by:	Wen Heping <wenheping at gmail.com>
This commit is contained in:
Martin Wilke 2009-05-28 23:36:10 +00:00
parent 7cf7e4315d
commit 043ce69d39
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=234730
6 changed files with 343 additions and 0 deletions

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@ -41,6 +41,7 @@
SUBDIR += lagan
SUBDIR += lamarc
SUBDIR += libgenome
SUBDIR += libsbml
SUBDIR += linux-foldingathome
SUBDIR += lsysexp
SUBDIR += mafft

56
biology/libsbml/Makefile Normal file
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@ -0,0 +1,56 @@
# New ports collection makefile for: libsbml
# Date created: 29 May, 2009
# Whom: Wen Heping <wenheping@gmail.com>
#
# $FreeBSD$
#
PORTNAME= libsbml
PORTVERSION= 3.3.2
CATEGORIES= biology devel
MASTER_SITES= SF
MASTER_SITE_SUBDIR= sbml
DISTNAME= ${PORTNAME}-${PORTVERSION}-src
MAINTAINER= wenheping@gmail.com
COMMENT= An API Library for Working with SBML File
LIB_DEPENDS= xml2.5:${PORTSDIR}/textproc/libxml2
OPTIONS= PYTHON "Support for Python" off \
RUBY "Support for Ruby" off
USE_GMAKE= yes
USE_ZIP= yes
GNU_CONFIGURE= yes
USE_LDCONFIG= yes
WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}
.include <bsd.port.pre.mk>
.if defined(WITH_PYTHON)
.include "../../Mk/bsd.python.mk"
BUILD_DEPENDS+= ${LOCALBASE}/bin/python:${PORTSDIR}/lang/python
CONFIGURE_ARGS+= --with-python
PLIST_SUB+= WITH_PYTHON="" \
SBML_EGGINFO=${PORTNAME}-${PORTVERSION}-${PYTHON_VERSION:S/thon//}.egg-info
.else
PLIST_SUB+= WITH_PYTHON="@comment "
.endif
.if defined(WITH_RUBY)
.include "../../Mk/bsd.ruby.mk"
BUILD_DEPENDS+= ${LOCALBASE}/bin/ruby:${PORTSDIR}/lang/ruby18
CONFIGURE_ARGS+= --with-ruby
PLIST_SUB+= WITH_RUBY=""
.else
PLIST_SUB+= WITH_RUBY="@comment "
.endif
post-install:
.if !defined(NOPORTEXAMPLES)
${MKDIR} ${EXAMPLESDIR}
cd ${WRKSRC}/examples \
&& ${FIND} . -type d -exec ${MKDIR} ${EXAMPLESDIR}/\{} \; \
&& ${FIND} . -type f -exec ${INSTALL_DATA} \{} ${EXAMPLESDIR}/\{} \;
.endif
.include <bsd.port.post.mk>

3
biology/libsbml/distinfo Normal file
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@ -0,0 +1,3 @@
MD5 (libsbml-3.3.2-src.zip) = f8b3ff297848f8cf0918c065f8a65133
SHA256 (libsbml-3.3.2-src.zip) = 5ebd8a57679fda954032e44111fdbcb8dc8598037354962d82a1742b621505d4
SIZE (libsbml-3.3.2-src.zip) = 7076694

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@ -0,0 +1,34 @@
--- Makefile.in.orig 2009-05-27 23:09:33.000000000 +0800
+++ Makefile.in 2009-05-27 23:33:47.000000000 +0800
@@ -413,7 +413,7 @@
endif
install-pc: libsbml.pc
- $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
+ $(INSTALL_SH) libsbml.pc -m 0644 "/usr/local/libdata/pkgconfig/libsbml.pc"
install-la: libsbml.la
ifeq "$(HOST_TYPE)" "cygwin"
@@ -449,17 +449,17 @@
$(warning $(uninstall-warning-msg))
uninstall-libsbml-pc:
- @target="$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"; \
+ @target="/usr/local/libdata/pkgconfig/libsbml.pc"; \
if test -f $$target ; then \
echo rm $$target; \
rm $$target; \
fi; \
- if test -d "$(DESTDIR)$(LIBDIR)/pkgconfig"; then \
+ if test -d "/usr/local/libdata/pkgconfig"; then \
if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
- echo rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
- rmdir "$(DESTDIR)$(LIBDIR)/pkgconfig"; \
+ echo rmdir "/usr/local/libdata/pkgconfig"; \
+ rmdir "/usr/local/libdata/pkgconfig"; \
else \
- echo "Directory $(DESTDIR)$(LIBDIR)/pkgconfig not empty; leaving it alone"; \
+ echo "Directory /usr/local/libdata/pkgconfig not empty; leaving it alone"; \
fi; \
fi;

11
biology/libsbml/pkg-descr Normal file
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@ -0,0 +1,11 @@
LibSBML is an open-source programming library to help you read, write,
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.
LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.
WWW: http://www.sbml.org/

238
biology/libsbml/pkg-plist Normal file
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@ -0,0 +1,238 @@
libdata/pkgconfig/libsbml.pc
include/sbml/Compartment.h
include/sbml/CompartmentType.h
include/sbml/Constraint.h
include/sbml/Delay.h
include/sbml/Event.h
include/sbml/EventAssignment.h
include/sbml/FunctionDefinition.h
include/sbml/InitialAssignment.h
include/sbml/KineticLaw.h
include/sbml/ListOf.h
include/sbml/Model.h
include/sbml/Parameter.h
include/sbml/Reaction.h
include/sbml/Rule.h
include/sbml/SBMLDocument.h
include/sbml/SBMLError.h
include/sbml/SBMLErrorLog.h
include/sbml/SBMLErrorTable.h
include/sbml/SBMLReader.h
include/sbml/SBMLTypeCodes.h
include/sbml/SBMLTypes.h
include/sbml/SBMLVisitor.h
include/sbml/SBMLWriter.h
include/sbml/SBO.h
include/sbml/SBase.h
include/sbml/Species.h
include/sbml/SpeciesReference.h
include/sbml/SpeciesType.h
include/sbml/StoichiometryMath.h
include/sbml/Trigger.h
include/sbml/Unit.h
include/sbml/UnitDefinition.h
include/sbml/UnitKind.h
include/sbml/annotation/CVTerm.h
include/sbml/annotation/ModelHistory.h
include/sbml/annotation/RDFAnnotation.h
include/sbml/common/common.h
include/sbml/common/extern.h
include/sbml/common/libsbml-config-unix.h
include/sbml/common/libsbml-config-win.h
include/sbml/common/libsbml-config.h
include/sbml/common/libsbml-version.h
include/sbml/common/sbmlfwd.h
include/sbml/compress/CompressCommon.h
include/sbml/compress/InputDecompressor.h
include/sbml/compress/OutputCompressor.h
include/sbml/compress/bzfstream.h
include/sbml/compress/crypt.h
include/sbml/compress/ioapi.h
include/sbml/compress/iowin32.h
include/sbml/compress/unzip.h
include/sbml/compress/zfstream.h
include/sbml/compress/zip.h
include/sbml/compress/zipfstream.h
include/sbml/math/ASTNode.h
include/sbml/math/FormulaFormatter.h
include/sbml/math/FormulaParser.h
include/sbml/math/FormulaTokenizer.h
include/sbml/math/MathML.h
include/sbml/units/FormulaUnitsData.h
include/sbml/units/UnitFormulaFormatter.h
include/sbml/units/UnitKindList.h
include/sbml/util/List.h
include/sbml/util/Stack.h
include/sbml/util/StringBuffer.h
include/sbml/util/memory.h
include/sbml/util/util.h
include/sbml/validator/ConsistencyValidator.h
include/sbml/validator/ConstraintMacros.h
include/sbml/validator/IdentifierConsistencyValidator.h
include/sbml/validator/InternalConsistencyValidator.h
include/sbml/validator/L1CompatibilityValidator.h
include/sbml/validator/L2v1CompatibilityValidator.h
include/sbml/validator/L2v2CompatibilityValidator.h
include/sbml/validator/L2v3CompatibilityValidator.h
include/sbml/validator/L2v4CompatibilityValidator.h
include/sbml/validator/MathMLConsistencyValidator.h
include/sbml/validator/ModelingPracticeValidator.h
include/sbml/validator/OverdeterminedValidator.h
include/sbml/validator/SBOConsistencyValidator.h
include/sbml/validator/UnitConsistencyValidator.h
include/sbml/validator/VConstraint.h
include/sbml/validator/Validator.h
include/sbml/validator/constraints/IdBase.h
include/sbml/validator/constraints/IdList.h
include/sbml/validator/constraints/MathMLBase.h
include/sbml/validator/constraints/OverDeterminedCheck.h
include/sbml/validator/constraints/UniqueIdBase.h
include/sbml/validator/constraints/UniqueMetaId.h
include/sbml/validator/constraints/UnitsBase.h
include/sbml/xml/LibXMLAttributes.h
include/sbml/xml/LibXMLHandler.h
include/sbml/xml/LibXMLNamespaces.h
include/sbml/xml/LibXMLParser.h
include/sbml/xml/LibXMLTranscode.h
include/sbml/xml/XMLAttributes.h
include/sbml/xml/XMLBuffer.h
include/sbml/xml/XMLError.h
include/sbml/xml/XMLErrorLog.h
include/sbml/xml/XMLExtern.h
include/sbml/xml/XMLFileBuffer.h
include/sbml/xml/XMLHandler.h
include/sbml/xml/XMLInputStream.h
include/sbml/xml/XMLMemoryBuffer.h
include/sbml/xml/XMLNamespaces.h
include/sbml/xml/XMLNode.h
include/sbml/xml/XMLOutputStream.h
include/sbml/xml/XMLParser.h
include/sbml/xml/XMLToken.h
include/sbml/xml/XMLTokenizer.h
include/sbml/xml/XMLTriple.h
lib/libsbml.3.3.2.so
lib/libsbml.so
lib/libsbml.a
@dirrm include/sbml/annotation
@dirrm include/sbml/common
@dirrm include/sbml/compress
@dirrm include/sbml/math
@dirrm include/sbml/units
@dirrm include/sbml/util
@dirrm include/sbml/validator/constraints
@dirrm include/sbml/validator
@dirrm include/sbml/xml
@dirrm include/sbml/
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/_libsbml.so
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.py
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml/libsbml.pyc
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/libsbml.pth
%%WITH_PYTHON%%%%PYTHON_SITELIBDIR%%/%%SBML_EGGINFO%%
%%WITH_PYTHON%%@dirrm %%PYTHON_SITELIBDIR%%/libsbml
%%WITH_RUBY%%%%RUBY_SITEARCHLIBDIR%%/libSBML.so
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/FormulaGraphvizFormatter.h
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/Makefile.in
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/convertSBML.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/drawMath.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/echoSBML.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/evaluateMath.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printMath.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/printSBML.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/readSBML.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/translateMath.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/util.h
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c/validateSBML.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/Makefile.in
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addCVTerms.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/addModelHistory.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/appendAnnotation.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/convertSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/createExampleSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/echoSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printAnnotation.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printMath.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printNotes.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/printUnits.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/readSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/translateMath.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetAnnotation.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/unsetNotes.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.c
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/util.h
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c++/validateSBML.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/Makefile.in
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/echoSBML.cs
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/csharp/validateSBML.cs
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/Makefile.in
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addCVTerms.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/addModelHistory.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/appendAnnotation.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/convertSBML.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/echoSBML.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/evaluateMath.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printAnnotation.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printMath.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printNotes.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printSBML.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/printUnits.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/readSBML.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/translateMath.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetAnnotation.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/unsetNotes.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/java/validateSBML.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/Makefile.in
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.java
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example1.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example2.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/example3.cpp
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/layout/layout2svg.xsl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/convertSBML.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/evaluateMath.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactionInfo.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/extractReactions.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printMath.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/printSBML.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/readSBML.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/translateMath.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/perl/validateSBML.pl
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/echoSBML.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/python/validateSBML.py
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/convertSBML.rb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/echoSBML.rb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/printMath.rb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ruby/validateSBML.rb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/README.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/algebraicrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/assignmentrules.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/boundarycondition.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/delay.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/dimerization.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/enzymekinetics.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/events.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/functiondef.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/multicomp.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/overdetermined.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/twodimensional.xml
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample-models/from-spec/level-2/units.xml
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/c++
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/csharp
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/java
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/layout
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/perl
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/python
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/ruby
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec/level-2
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models/from-spec
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sample-models
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%