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| author | yuri <yuri@FreeBSD.org> | 2018-09-21 16:04:50 +0800 |
|---|---|---|
| committer | yuri <yuri@FreeBSD.org> | 2018-09-21 16:04:50 +0800 |
| commit | 97def3ffdb88e7075fe5553b58ca299fa593fe1d (patch) | |
| tree | bb9f386d1b26851520797969bec53649e048705b /biology | |
| parent | f54ef5298167891d2940fa830f393f2dcfab9527 (diff) | |
| download | freebsd-ports-gnome-97def3ffdb88e7075fe5553b58ca299fa593fe1d.tar.gz freebsd-ports-gnome-97def3ffdb88e7075fe5553b58ca299fa593fe1d.tar.zst freebsd-ports-gnome-97def3ffdb88e7075fe5553b58ca299fa593fe1d.zip | |
New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-loompy/Makefile | 24 | ||||
| -rw-r--r-- | biology/py-loompy/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-loompy/pkg-descr | 16 |
4 files changed, 44 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index c4803253114f..b9f804fdcab7 100644 --- a/biology/Makefile +++ b/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 diff --git a/biology/py-loompy/Makefile b/biology/py-loompy/Makefile new file mode 100644 index 000000000000..5878058309bc --- /dev/null +++ b/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> diff --git a/biology/py-loompy/distinfo b/biology/py-loompy/distinfo new file mode 100644 index 000000000000..2fcdb351106c --- /dev/null +++ b/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 diff --git a/biology/py-loompy/pkg-descr b/biology/py-loompy/pkg-descr new file mode 100644 index 000000000000..65d3e8d7f75d --- /dev/null +++ b/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/ |