3 files changed, 47 insertions, 0 deletions

diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile
new file mode 100644
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+++ b/biology/py-biom-format/Makefile
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+# Created by: Joseph Mingrone <jrm@ftfl.ca>
+# $FreeBSD$
+
+PORTNAME=	biom-format
+PORTVERSION=	2.1.5
+CATEGORIES=	biology python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jrm@ftfl.ca
+COMMENT=	Biological Observation Matrix (BIOM) Format Project
+
+LICENSE=	BSD3CLAUSE
+
+BUILD_DEPENDS=	${PYNUMPY}
+RUN_DEPENDS=	${PYNUMPY} ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	biocore
+
+USES=		python
+USE_PYTHON=	autoplist distutils
+
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biom/*.so
+
+.include <bsd.port.mk>
diff --git a/biology/py-biom-format/distinfo b/biology/py-biom-format/distinfo
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index 000000000000..50be5f77ff2b
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+++ b/biology/py-biom-format/distinfo
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+SHA256 (biocore-biom-format-2.1.5_GH0.tar.gz) = e808db612291536e3ca2297c6d72b99154a324fb55fb8898baabc71ceee045d8
+SIZE (biocore-biom-format-2.1.5_GH0.tar.gz) = 11963101
diff --git a/biology/py-biom-format/pkg-descr b/biology/py-biom-format/pkg-descr
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+++ b/biology/py-biom-format/pkg-descr
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+The BIOM file format (canonically pronounced biome) is designed to be a
+general-use format for representing biological sample by observation contingency
+tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
+Genomics Standards Consortium supported project.
+
+The BIOM format is designed for general use in broad areas of comparative
+-omics. For example, in marker-gene surveys, the primary use of this format is
+to represent OTU tables: the observations in this case are OTUs and the matrix
+contains counts corresponding to the number of times each OTU is observed in
+each sample. With respect to metagenome data, this format would be used to
+represent metagenome tables: the observations in this case might correspond to
+SEED subsystems, and the matrix would contain counts corresponding to the number
+of times each subsystem is observed in each metagenome. Similarly, with respect
+to genome data, this format may be used to represent a set of genomes: the
+observations in this case again might correspond to SEED subsystems, and the
+counts would correspond to the number of times each subsystem is observed in
+each genome.
+
+WWW: http://biom-format.org