diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-biom-format/Makefile | 26 | ||||
| -rw-r--r-- | biology/py-biom-format/distinfo | 2 | ||||
| -rw-r--r-- | biology/py-biom-format/pkg-descr | 19 |
4 files changed, 48 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index d8ff8900e298..97cdac5ece8c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -80,6 +80,7 @@ SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 + SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile new file mode 100644 index 000000000000..adb20e4c7484 --- /dev/null +++ b/biology/py-biom-format/Makefile @@ -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> diff --git a/biology/py-biom-format/distinfo b/biology/py-biom-format/distinfo new file mode 100644 index 000000000000..50be5f77ff2b --- /dev/null +++ b/biology/py-biom-format/distinfo @@ -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 diff --git a/biology/py-biom-format/pkg-descr b/biology/py-biom-format/pkg-descr new file mode 100644 index 000000000000..2b0a35032361 --- /dev/null +++ b/biology/py-biom-format/pkg-descr @@ -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 |