svn commit: r414865 - in head/biology: . py-biom-format

[Olivier Duchateau]

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 at ftfl.ca>
+# $FreeBSD$
+
+PORTNAME=	biom-format
+PORTVERSION=	2.1.5
+CATEGORIES=	biology python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jrm at 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