Date: Mon, 9 May 2016 16:37:44 +0000 (UTC) From: Olivier Duchateau <olivierd@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r414865 - in head/biology: . py-biom-format Message-ID: <201605091637.u49GbiY0040581@repo.freebsd.org>
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Author: olivierd Date: Mon May 9 16:37:44 2016 New Revision: 414865 URL: https://svnweb.freebsd.org/changeset/ports/414865 Log: 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/ PR: 209193 Submitted by: Joseph Mingrone Added: head/biology/py-biom-format/ head/biology/py-biom-format/Makefile (contents, props changed) head/biology/py-biom-format/distinfo (contents, props changed) head/biology/py-biom-format/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Mon May 9 16:23:32 2016 (r414864) +++ head/biology/Makefile Mon May 9 16:37:44 2016 (r414865) @@ -80,6 +80,7 @@ SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 + SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta Added: head/biology/py-biom-format/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-biom-format/Makefile Mon May 9 16:37:44 2016 (r414865) @@ -0,0 +1,26 @@ +# 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> Added: head/biology/py-biom-format/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-biom-format/distinfo Mon May 9 16:37:44 2016 (r414865) @@ -0,0 +1,2 @@ +SHA256 (biocore-biom-format-2.1.5_GH0.tar.gz) = e808db612291536e3ca2297c6d72b99154a324fb55fb8898baabc71ceee045d8 +SIZE (biocore-biom-format-2.1.5_GH0.tar.gz) = 11963101 Added: head/biology/py-biom-format/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/py-biom-format/pkg-descr Mon May 9 16:37:44 2016 (r414865) @@ -0,0 +1,19 @@ +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
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