New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data

svn path=/head/; revision=480236

biology/Makefile

@@ -103,6 +103,7 @@
     SUBDIR += py-biopython
     SUBDIR += py-bx-python
     SUBDIR += py-cutadapt
+    SUBDIR += py-loompy
     SUBDIR += py-macs2
     SUBDIR += py-orange3-bioinformatics
     SUBDIR += py-orange3-single-cell

biology/py-loompy/Makefile

@@ -0,0 +1,24 @@
+# $FreeBSD$
+
+PORTNAME=	loompy
+DISTVERSION=	2.0.14
+CATEGORIES=	biology python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Work with .loom files for single-cell RNA-seq data
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
+
+USES=		python:3.6+
+USE_PYTHON=	distutils autoplist
+NO_ARCH=	yes
+
+.include <bsd.port.mk>

biology/py-loompy/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1537516516
+SHA256 (loompy-2.0.14.tar.gz) = 9ffc5e717d7932d72f80a301bef3a9a8d62b84ecf379c4b1ffd750f6b1388e88
+SIZE (loompy-2.0.14.tar.gz) = 30942

biology/py-loompy/pkg-descr

@@ -0,0 +1,16 @@
+Loom is an efficient file format for large omics datasets. Loom files contain
+a main matrix, optional additional layers, a variable number of row and column
+annotations, and sparse graph objects. Under the hood, Loom files are HDF5 and
+can be opened from many programming languages, including Python, R, C, C++,
+Java, MATLAB, Mathematica, and Julia.
+
+Key features:
+* Single file that can be moved around
+* Metadata travels with the main data
+* Data, clustering, layout, annotation stored together
+* Efficient random access
+* Automatic, on-the-fly compression
+* Out-of-memory data processing
+* Open source, BSD license
+
+WWW: https://loompy.org/