diff options
author | Johann Visagie <wjv@FreeBSD.org> | 2001-09-06 12:42:36 +0000 |
---|---|---|
committer | Johann Visagie <wjv@FreeBSD.org> | 2001-09-06 12:42:36 +0000 |
commit | 5f3039ab6076092726b854406105df809b1635ad (patch) | |
tree | 759bb416619015aa2d4bb3c3b977f0d150ccfb24 /biology/py-biopython | |
parent | Upgrade to 2.5. (diff) |
- Update to version 1.00.a3
- Use pkg-req to check the installed version of Python
Notes
Notes:
svn path=/head/; revision=47471
Diffstat (limited to 'biology/py-biopython')
-rw-r--r-- | biology/py-biopython/Makefile | 41 | ||||
-rw-r--r-- | biology/py-biopython/distinfo | 2 | ||||
-rw-r--r-- | biology/py-biopython/pkg-plist | 212 | ||||
-rw-r--r-- | biology/py-biopython/pkg-req | 17 |
4 files changed, 167 insertions, 105 deletions
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index e59a64a4cae6..2787d9a959ea 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.00.a2 +PORTVERSION= 1.00.a3 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/Download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -17,16 +17,14 @@ MAINTAINER= wjv@FreeBSD.org BUILD_DEPENDS= ${PYDISTUTILS} RUN_DEPENDS= ${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \ - ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric - -# Biopython requires Python 2.0 or above: -PYTHON_VERSION= python2.1 + ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric \ + ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base +USE_PYTHON= yes PLIST_SUB+= PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \ PLIST_FNORB=${PLIST_FNORB} CPIO= cpio --quiet -pdum -R -DOCDIR= ${PREFIX}/share/doc/py-biopython -EGDIR= ${PREFIX}/share/examples/py-biopython +EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME} # CORBA support (a.k.a Biopython-CORBA): # Set WITH_CORBA to enable CORBA support for the Biopython port. @@ -41,7 +39,7 @@ EGDIR= ${PREFIX}/share/examples/py-biopython # - ORBit is a very popular and elegant ORB. The ORBit-Python bindings are # used. # Since Fnorb is distributed under a non-free licence and ORBit support in -# Biopython-CORBA is not yet stable, "omniorb" is the default. +# Biopython-CORBA is reputedly not yet stable, "omniorb" is the default. CORBA_ORB?= omniorb CORBA_VERSION= 0.2.1 @@ -57,6 +55,7 @@ PLIST_OMNIORB= "" PLIST_FNORB= "@comment " .elif ${CORBA_ORB} == "fnorb" BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb +RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb CORBA_ORBNAME= Fnorb EXTRA_PATCHES+= ${PATCHDIR}/extra-patch-build_helper.py PLIST_OMNIORB= "@comment " @@ -92,6 +91,9 @@ do-build: @ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py build .endif +pre-install: + @ ${SH} ${PKGREQ} INSTALL + do-install: @ cd ${WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \ --prefix=${PREFIX} @@ -102,24 +104,25 @@ do-install: post-install: .if !defined(NOPORTDOCS) - @ ${MKDIR} ${DOCDIR} + @ ${MKDIR} ${DOCSDIR} .for docfiles in *.txt *.tex *.py - @ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCDIR} + @ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR} .endfor - @ ${MKDIR} ${EGDIR} - @ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EGDIR} + @ ${MKDIR} ${EXAMPLESDIR} + @ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EXAMPLESDIR} @ cd ${WRKSRC} && find Scripts \ - | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR} + | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR} .if defined(WITH_CORBA) - @ ${MKDIR} ${DOCDIR}/BioCorba + @ ${MKDIR} ${DOCSDIR}/BioCorba .for docfiles in *.tex *.pdf - @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCDIR}/BioCorba + @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba .endfor - @ ${MKDIR} ${EGDIR}/BioCorba + @ ${MKDIR} ${EXAMPLESDIR}/BioCorba @ cd ${CORBA_WRKSRC}/Doc/examples && find * \ - | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}/BioCorba - @ ${MKDIR} ${EGDIR}/BioCorba/Scripts - @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* ${EGDIR}/BioCorba/Scripts + | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}/BioCorba + @ ${MKDIR} ${EXAMPLESDIR}/BioCorba/Scripts + @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \ + ${EXAMPLESDIR}/BioCorba/Scripts .endif # defined(WITH_CORBA) .endif # !defined(NOPORTDOCS) diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo index 5627a525c266..d88599879874 100644 --- a/biology/py-biopython/distinfo +++ b/biology/py-biopython/distinfo @@ -1,2 +1,2 @@ -MD5 (biopython-1.00a2.tar.gz) = 416fb1ab08dfdd7f3d4d75bc0043ace8 +MD5 (biopython-1.00a3.tar.gz) = be59a12eeb2c0bcdd82a73dfd7bcc615 MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25 diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist index a7b709a312f1..8a4749f0eb0b 100644 --- a/biology/py-biopython/pkg-plist +++ b/biology/py-biopython/pkg-plist @@ -201,73 +201,74 @@ %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.py %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyc %%PLIST_OMNIORB%%lib/%%PYTHON_VERSION%%/site-packages/BioCorba/ensembl_idl.pyo -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.pdf -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/IntroPythonClient.tex -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.pdf -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/README.tex -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.pdf -%%PORTDOCS%%%%PLIST_CORBA%%share/doc/py-biopython/BioCorba/biocorbahowto.tex -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/Scripts/bioenv_server.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.fasta -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/a_drought.gb -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/embl_biocorba.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_bioenv.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_biopy.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_pseqit.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/fasta_server.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gb_bioenv.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbclient.py -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/gbsrv.pl -%%PORTDOCS%%%%PLIST_CORBA%%share/examples/py-biopython/BioCorba/genbank_db_server.py -%%PORTDOCS%%share/doc/py-biopython/Blast.txt -%%PORTDOCS%%share/doc/py-biopython/Enzyme.txt -%%PORTDOCS%%share/doc/py-biopython/Fasta.txt -%%PORTDOCS%%share/doc/py-biopython/Medline.txt -%%PORTDOCS%%share/doc/py-biopython/Parser.txt -%%PORTDOCS%%share/doc/py-biopython/Prosite.txt -%%PORTDOCS%%share/doc/py-biopython/References.txt -%%PORTDOCS%%share/doc/py-biopython/SCOP.txt -%%PORTDOCS%%share/doc/py-biopython/SwissProt.txt -%%PORTDOCS%%share/doc/py-biopython/Tutorial.tex -%%PORTDOCS%%share/doc/py-biopython/Tutorial.txt -%%PORTDOCS%%share/doc/py-biopython/make_api_docs.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/SeqGui/SeqGui.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/query_pubmed.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/README -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/nextorf.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/test.fas -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/testrp.fas -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blast.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_blastbg.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_io.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_sequence.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_translations.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_utils.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbb_widget.py -%%PORTDOCS%%share/examples/py-biopython/Scripts/xbbtools/xbbtools.py -%%PORTDOCS%%share/examples/py-biopython/clustal_run.py -%%PORTDOCS%%share/examples/py-biopython/fasta_consumer.py -%%PORTDOCS%%share/examples/py-biopython/fasta_dictionary.py -%%PORTDOCS%%share/examples/py-biopython/fasta_iterator.py -%%PORTDOCS%%share/examples/py-biopython/getgene.py -%%PORTDOCS%%share/examples/py-biopython/local_blast.py -%%PORTDOCS%%share/examples/py-biopython/make_subsmat.py -%%PORTDOCS%%share/examples/py-biopython/pubmed_search.py -%%PORTDOCS%%share/examples/py-biopython/query_entrez.py -%%PORTDOCS%%share/examples/py-biopython/swissprot.py -%%PORTDOCS%%share/examples/py-biopython/www_blast.py +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.pdf +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/IntroPythonClient.tex +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.pdf +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/README.tex +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.pdf +%%PORTDOCS%%%%PLIST_CORBA%%share/doc/biopython/BioCorba/biocorbahowto.tex +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_client.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyFirstClient/secret_message_idl.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_client.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/biosequence_idl.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA/__init__.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_client.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo_idl.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/Scripts/bioenv_server.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.fasta +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/a_drought.gb +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/embl_biocorba.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_bioenv.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_biopy.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_pseqit.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/fasta_server.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gb_bioenv.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbclient.py +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/gbsrv.pl +%%PORTDOCS%%%%PLIST_CORBA%%share/examples/biopython/BioCorba/genbank_db_server.py +%%PORTDOCS%%share/doc/biopython/Blast.txt +%%PORTDOCS%%share/doc/biopython/Enzyme.txt +%%PORTDOCS%%share/doc/biopython/Fasta.txt +%%PORTDOCS%%share/doc/biopython/KEGG.txt +%%PORTDOCS%%share/doc/biopython/Medline.txt +%%PORTDOCS%%share/doc/biopython/Parser.txt +%%PORTDOCS%%share/doc/biopython/Prosite.txt +%%PORTDOCS%%share/doc/biopython/References.txt +%%PORTDOCS%%share/doc/biopython/SCOP.txt +%%PORTDOCS%%share/doc/biopython/SwissProt.txt +%%PORTDOCS%%share/doc/biopython/Tutorial.tex +%%PORTDOCS%%share/doc/biopython/Tutorial.txt +%%PORTDOCS%%share/doc/biopython/make_api_docs.py +%%PORTDOCS%%share/examples/biopython/Scripts/SeqGui/SeqGui.py +%%PORTDOCS%%share/examples/biopython/Scripts/query_pubmed.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/README +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/nextorf.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/test.fas +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/testrp.fas +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blast.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_blastbg.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_io.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_sequence.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_translations.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_utils.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbb_widget.py +%%PORTDOCS%%share/examples/biopython/Scripts/xbbtools/xbbtools.py +%%PORTDOCS%%share/examples/biopython/clustal_run.py +%%PORTDOCS%%share/examples/biopython/fasta_consumer.py +%%PORTDOCS%%share/examples/biopython/fasta_dictionary.py +%%PORTDOCS%%share/examples/biopython/fasta_iterator.py +%%PORTDOCS%%share/examples/biopython/getgene.py +%%PORTDOCS%%share/examples/biopython/local_blast.py +%%PORTDOCS%%share/examples/biopython/make_subsmat.py +%%PORTDOCS%%share/examples/biopython/pubmed_search.py +%%PORTDOCS%%share/examples/biopython/query_entrez.py +%%PORTDOCS%%share/examples/biopython/swissprot.py +%%PORTDOCS%%share/examples/biopython/www_blast.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/AlignInfo.pyo @@ -280,6 +281,15 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/Generic.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/pairwise.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/support.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/IUPAC.pyo @@ -358,6 +368,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound/compound_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/Record.pyo @@ -445,6 +473,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/SProt.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/NaiveBayes.pyo @@ -464,6 +495,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/kMeans.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Clustering/xkMeans.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/MultiProc/Scheduler.pyo @@ -521,6 +555,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/sequtils.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.py lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo @@ -540,6 +577,10 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta @@ -552,24 +593,24 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Align @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/Scripts -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient/idl_demo -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyThirdClient -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers__POA -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient/servers -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MySecondClient -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient/messenger -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient/MyFirstClient -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba/IntroClient -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/py-biopython/BioCorba -%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/py-biopython/BioCorba -%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/xbbtools -%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts/SeqGui -%%PORTDOCS%%@dirrm share/examples/py-biopython/Scripts -%%PORTDOCS%%@dirrm share/examples/py-biopython -%%PORTDOCS%%@dirrm share/doc/py-biopython +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/Scripts +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo__POA +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient/idl_demo +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyThirdClient +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers__POA +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient/servers +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MySecondClient +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger__POA +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient/messenger +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient/MyFirstClient +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba/IntroClient +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/examples/biopython/BioCorba +%%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/biopython/BioCorba +%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/xbbtools +%%PORTDOCS%%@dirrm share/examples/biopython/Scripts/SeqGui +%%PORTDOCS%%@dirrm share/examples/biopython/Scripts +%%PORTDOCS%%@dirrm share/examples/biopython +%%PORTDOCS%%@dirrm share/doc/biopython %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/ensembl_skel %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel/seqcore_skel %%PLIST_FNORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/org_skel/biocorba_skel @@ -597,3 +638,4 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.pyo %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Bio %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/Adapters %%PLIST_CORBA%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba + diff --git a/biology/py-biopython/pkg-req b/biology/py-biopython/pkg-req new file mode 100644 index 000000000000..481af4e9a7ad --- /dev/null +++ b/biology/py-biopython/pkg-req @@ -0,0 +1,17 @@ +#!/bin/sh + +PATH=$PATH:/usr/local/bin + +if [ "x$1" = "xINSTALL" -o "x$2" = "xINSTALL" ]; then + PYTHON_GT=`python -c 'import string, sys; \ + print string.split(sys.version)[0] >= "2.0"'` + if [ "x${PYTHON_GT}" = "x1" ]; then + exit 0 + else + echo "-----------------------------------------------------------" + echo "Biopython requires Python version 2.0 or greater - " + echo " please update your Python installation before proceeding." + echo "-----------------------------------------------------------" + exit 1 + fi +fi |