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py-biopython: Collection of Python modules for bioinformatics
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Mon Nov 5 14:47:54 2018 -0600
Changeset: 6398725d833732f9660a66302b1f20e35cc53c08
Modified Files:
Makefile
Added Files:
py-biopython/DESCR
py-biopython/Makefile
py-biopython/PLIST
py-biopython/distinfo
Log Message:
py-biopython: Collection of Python modules for bioinformatics
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6398725d833732f9660a66302b1f20e35cc53c08
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
py-biopython/DESCR | 10 +
py-biopython/Makefile | 31 ++
py-biopython/PLIST | 1282 +++++++++++++++++++++++++++++++++++++++++++++++++
py-biopython/distinfo | 6 +
5 files changed, 1330 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 8e40ec7344..ce27931824 100644
--- a/Makefile
+++ b/Makefile
@@ -3047,6 +3047,7 @@ SUBDIR+= py-bidict
SUBDIR+= py-bigfloat
SUBDIR+= py-bintrees
SUBDIR+= py-biofrills
+SUBDIR+= py-biopython
SUBDIR+= py-bip
SUBDIR+= py-biskit
SUBDIR+= py-bitarray
diff --git a/py-biopython/DESCR b/py-biopython/DESCR
new file mode 100644
index 0000000000..38b785a7de
--- /dev/null
+++ b/py-biopython/DESCR
@@ -0,0 +1,10 @@
+The Biopython Project is an international association of developers who are
+providing freely available Python tools for use in areas of computational
+molecular biology such as bioinformatics and genomics.
+Biopython is a collection of Python packages and modules created by the
+Biopython Project, intended to provide the basis for building bioinformatics
+applications in the Python language.
+Note that the current release is alpha quality, and not yet deemed to be
+stable.
+This port includes optional support for Biopython-CORBA, a CORBA interface
+built to the BioCorba standard (http://biocorba.org/).
diff --git a/py-biopython/Makefile b/py-biopython/Makefile
new file mode 100644
index 0000000000..5d8b4e4575
--- /dev/null
+++ b/py-biopython/Makefile
@@ -0,0 +1,31 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Mon Nov 5 14:38:46 CST 2018 #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#pre-configure: # unbreak for python3: README.rst can't be decoded with the ascii codec: https://github.com/biopython/biopython/issues/1649
+# @truncate -s 0 ${WRKSRC}/README.rst
+
+DISTNAME= biopython-${PV}
+PKGNAME= ${PYPKGPREFIX}-biopython-${PV}
+CATEGORIES= biology
+MASTER_SITES= http://www.biopython.org/DIST/
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://biopython.org/
+COMMENT= Collection of Python modules for bioinformatics
+LICENSE= modified-bsd
+
+# Many dependencies. Option?
+# DEPENDS+= ${PYPKGPREFIX}-reportlab>0:../../print/py-reportlab
+DEPENDS+= ${PYPKGPREFIX}-numpy>0:../../math/py-numpy
+
+PV= 1.72
+
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-biopython/PLIST b/py-biopython/PLIST
new file mode 100644
index 0000000000..7715a6509b
--- /dev/null
+++ b/py-biopython/PLIST
@@ -0,0 +1,1282 @@
+@comment $NetBSD$
+${PYSITELIB}/Bio/Affy/CelFile.py
+${PYSITELIB}/Bio/Affy/CelFile.pyc
+${PYSITELIB}/Bio/Affy/CelFile.pyo
+${PYSITELIB}/Bio/Affy/__init__.py
+${PYSITELIB}/Bio/Affy/__init__.pyc
+${PYSITELIB}/Bio/Affy/__init__.pyo
+${PYSITELIB}/Bio/Align/AlignInfo.py
+${PYSITELIB}/Bio/Align/AlignInfo.pyc
+${PYSITELIB}/Bio/Align/AlignInfo.pyo
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.py
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyc
+${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyo
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.py
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyc
+${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyo
+${PYSITELIB}/Bio/Align/Applications/_Dialign.py
+${PYSITELIB}/Bio/Align/Applications/_Dialign.pyc
+${PYSITELIB}/Bio/Align/Applications/_Dialign.pyo
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.py
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyc
+${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyo
+${PYSITELIB}/Bio/Align/Applications/_Mafft.py
+${PYSITELIB}/Bio/Align/Applications/_Mafft.pyc
+${PYSITELIB}/Bio/Align/Applications/_Mafft.pyo
+${PYSITELIB}/Bio/Align/Applications/_Muscle.py
+${PYSITELIB}/Bio/Align/Applications/_Muscle.pyc
+${PYSITELIB}/Bio/Align/Applications/_Muscle.pyo
+${PYSITELIB}/Bio/Align/Applications/_Prank.py
+${PYSITELIB}/Bio/Align/Applications/_Prank.pyc
+${PYSITELIB}/Bio/Align/Applications/_Prank.pyo
+${PYSITELIB}/Bio/Align/Applications/_Probcons.py
+${PYSITELIB}/Bio/Align/Applications/_Probcons.pyc
+${PYSITELIB}/Bio/Align/Applications/_Probcons.pyo
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.py
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyc
+${PYSITELIB}/Bio/Align/Applications/_TCoffee.pyo
+${PYSITELIB}/Bio/Align/Applications/__init__.py
+${PYSITELIB}/Bio/Align/Applications/__init__.pyc
+${PYSITELIB}/Bio/Align/Applications/__init__.pyo
+${PYSITELIB}/Bio/Align/__init__.py
+${PYSITELIB}/Bio/Align/__init__.pyc
+${PYSITELIB}/Bio/Align/__init__.pyo
+${PYSITELIB}/Bio/Align/_aligners.so
+${PYSITELIB}/Bio/AlignIO/ClustalIO.py
+${PYSITELIB}/Bio/AlignIO/ClustalIO.pyc
+${PYSITELIB}/Bio/AlignIO/ClustalIO.pyo
+${PYSITELIB}/Bio/AlignIO/EmbossIO.py
+${PYSITELIB}/Bio/AlignIO/EmbossIO.pyc
+${PYSITELIB}/Bio/AlignIO/EmbossIO.pyo
+${PYSITELIB}/Bio/AlignIO/FastaIO.py
+${PYSITELIB}/Bio/AlignIO/FastaIO.pyc
+${PYSITELIB}/Bio/AlignIO/FastaIO.pyo
+${PYSITELIB}/Bio/AlignIO/Interfaces.py
+${PYSITELIB}/Bio/AlignIO/Interfaces.pyc
+${PYSITELIB}/Bio/AlignIO/Interfaces.pyo
+${PYSITELIB}/Bio/AlignIO/MafIO.py
+${PYSITELIB}/Bio/AlignIO/MafIO.pyc
+${PYSITELIB}/Bio/AlignIO/MafIO.pyo
+${PYSITELIB}/Bio/AlignIO/MauveIO.py
+${PYSITELIB}/Bio/AlignIO/MauveIO.pyc
+${PYSITELIB}/Bio/AlignIO/MauveIO.pyo
+${PYSITELIB}/Bio/AlignIO/NexusIO.py
+${PYSITELIB}/Bio/AlignIO/NexusIO.pyc
+${PYSITELIB}/Bio/AlignIO/NexusIO.pyo
+${PYSITELIB}/Bio/AlignIO/PhylipIO.py
+${PYSITELIB}/Bio/AlignIO/PhylipIO.pyc
+${PYSITELIB}/Bio/AlignIO/PhylipIO.pyo
+${PYSITELIB}/Bio/AlignIO/StockholmIO.py
+${PYSITELIB}/Bio/AlignIO/StockholmIO.pyc
+${PYSITELIB}/Bio/AlignIO/StockholmIO.pyo
+${PYSITELIB}/Bio/AlignIO/__init__.py
+${PYSITELIB}/Bio/AlignIO/__init__.pyc
+${PYSITELIB}/Bio/AlignIO/__init__.pyo
+${PYSITELIB}/Bio/Alphabet/IUPAC.py
+${PYSITELIB}/Bio/Alphabet/IUPAC.pyc
+${PYSITELIB}/Bio/Alphabet/IUPAC.pyo
+${PYSITELIB}/Bio/Alphabet/Reduced.py
+${PYSITELIB}/Bio/Alphabet/Reduced.pyc
+${PYSITELIB}/Bio/Alphabet/Reduced.pyo
+${PYSITELIB}/Bio/Alphabet/__init__.py
+${PYSITELIB}/Bio/Alphabet/__init__.pyc
+${PYSITELIB}/Bio/Alphabet/__init__.pyo
+${PYSITELIB}/Bio/Application/__init__.py
+${PYSITELIB}/Bio/Application/__init__.pyc
+${PYSITELIB}/Bio/Application/__init__.pyo
+${PYSITELIB}/Bio/Blast/Applications.py
+${PYSITELIB}/Bio/Blast/Applications.pyc
+${PYSITELIB}/Bio/Blast/Applications.pyo
+${PYSITELIB}/Bio/Blast/NCBIStandalone.py
+${PYSITELIB}/Bio/Blast/NCBIStandalone.pyc
+${PYSITELIB}/Bio/Blast/NCBIStandalone.pyo
+${PYSITELIB}/Bio/Blast/NCBIWWW.py
+${PYSITELIB}/Bio/Blast/NCBIWWW.pyc
+${PYSITELIB}/Bio/Blast/NCBIWWW.pyo
+${PYSITELIB}/Bio/Blast/NCBIXML.py
+${PYSITELIB}/Bio/Blast/NCBIXML.pyc
+${PYSITELIB}/Bio/Blast/NCBIXML.pyo
+${PYSITELIB}/Bio/Blast/ParseBlastTable.py
+${PYSITELIB}/Bio/Blast/ParseBlastTable.pyc
+${PYSITELIB}/Bio/Blast/ParseBlastTable.pyo
+${PYSITELIB}/Bio/Blast/Record.py
+${PYSITELIB}/Bio/Blast/Record.pyc
+${PYSITELIB}/Bio/Blast/Record.pyo
+${PYSITELIB}/Bio/Blast/__init__.py
+${PYSITELIB}/Bio/Blast/__init__.pyc
+${PYSITELIB}/Bio/Blast/__init__.pyo
+${PYSITELIB}/Bio/CAPS/__init__.py
+${PYSITELIB}/Bio/CAPS/__init__.pyc
+${PYSITELIB}/Bio/CAPS/__init__.pyo
+${PYSITELIB}/Bio/Cluster/__init__.py
+${PYSITELIB}/Bio/Cluster/__init__.pyc
+${PYSITELIB}/Bio/Cluster/__init__.pyo
+${PYSITELIB}/Bio/Cluster/_cluster.so
+${PYSITELIB}/Bio/Compass/__init__.py
+${PYSITELIB}/Bio/Compass/__init__.pyc
+${PYSITELIB}/Bio/Compass/__init__.pyo
+${PYSITELIB}/Bio/Crystal/__init__.py
+${PYSITELIB}/Bio/Crystal/__init__.pyc
+${PYSITELIB}/Bio/Crystal/__init__.pyo
+${PYSITELIB}/Bio/Data/CodonTable.py
+${PYSITELIB}/Bio/Data/CodonTable.pyc
+${PYSITELIB}/Bio/Data/CodonTable.pyo
+${PYSITELIB}/Bio/Data/IUPACData.py
+${PYSITELIB}/Bio/Data/IUPACData.pyc
+${PYSITELIB}/Bio/Data/IUPACData.pyo
+${PYSITELIB}/Bio/Data/SCOPData.py
+${PYSITELIB}/Bio/Data/SCOPData.pyc
+${PYSITELIB}/Bio/Data/SCOPData.pyo
+${PYSITELIB}/Bio/Data/__init__.py
+${PYSITELIB}/Bio/Data/__init__.pyc
+${PYSITELIB}/Bio/Data/__init__.pyo
+${PYSITELIB}/Bio/Emboss/Applications.py
+${PYSITELIB}/Bio/Emboss/Applications.pyc
+${PYSITELIB}/Bio/Emboss/Applications.pyo
+${PYSITELIB}/Bio/Emboss/Primer3.py
+${PYSITELIB}/Bio/Emboss/Primer3.pyc
+${PYSITELIB}/Bio/Emboss/Primer3.pyo
+${PYSITELIB}/Bio/Emboss/PrimerSearch.py
+${PYSITELIB}/Bio/Emboss/PrimerSearch.pyc
+${PYSITELIB}/Bio/Emboss/PrimerSearch.pyo
+${PYSITELIB}/Bio/Emboss/__init__.py
+${PYSITELIB}/Bio/Emboss/__init__.pyc
+${PYSITELIB}/Bio/Emboss/__init__.pyo
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/Docsum_3_4.dtd
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+${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/EMBL_General.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/GenBank_General.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/HomoloGene.mod.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.dtd
+${PYSITELIB}/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd
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diff --git a/py-biopython/distinfo b/py-biopython/distinfo
new file mode 100644
index 0000000000..ae567611c4
--- /dev/null
+++ b/py-biopython/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (biopython-1.72.tar.gz) = 9957c0856a29c194a5e421642f53c5ab3595a08e
+RMD160 (biopython-1.72.tar.gz) = 8d3659c93a8d6c916ea242a2ae689609879454ce
+SHA512 (biopython-1.72.tar.gz) = e2ce74f4533c9c779c8fbafb73ed562c890209a4318fc9d8616ec98670ee5e97649b8c1b0207c91454b923faecf375f20bd6a0aaff52ccc73268fb0b1ea0b44c
+Size (biopython-1.72.tar.gz) = 16391360 bytes
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