diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/libsbml/Makefile | 56 | ||||
| -rw-r--r-- | biology/libsbml/distinfo | 3 | ||||
| -rw-r--r-- | biology/libsbml/files/patch-Makefile.in | 34 | ||||
| -rw-r--r-- | biology/libsbml/pkg-descr | 11 | ||||
| -rw-r--r-- | biology/libsbml/pkg-plist | 238 |
6 files changed, 343 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 1a9b5e34ef95..892e117aa36c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -41,6 +41,7 @@ SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgenome + SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += lsysexp SUBDIR += mafft diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile new file mode 100644 index 000000000000..fa61cf8294e4 --- /dev/null +++ b/biology/libsbml/Makefile @@ -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> diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo new file mode 100644 index 000000000000..a54dd0635d09 --- /dev/null +++ b/biology/libsbml/distinfo @@ -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 diff --git a/biology/libsbml/files/patch-Makefile.in b/biology/libsbml/files/patch-Makefile.in new file mode 100644 index 000000000000..309111070348 --- /dev/null +++ b/biology/libsbml/files/patch-Makefile.in @@ -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; + diff --git a/biology/libsbml/pkg-descr b/biology/libsbml/pkg-descr new file mode 100644 index 000000000000..b013d3cc7730 --- /dev/null +++ b/biology/libsbml/pkg-descr @@ -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/ diff --git a/biology/libsbml/pkg-plist b/biology/libsbml/pkg-plist new file mode 100644 index 000000000000..5a337b1f66fb --- /dev/null +++ b/biology/libsbml/pkg-plist @@ -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%% |