Port details on branch 2022Q2 |
- py-loompy Work with .loom files for single-cell RNA-seq data
- 3.0.7_1 biology =0 3.0.7_1Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2018-09-21 08:05:03
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- Also Listed In: python
- License: BSD2CLAUSE
- WWW:
- https://loompy.org/
- Description:
- 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
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}loompy>0:biology/py-loompy@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-loompy/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-loompy
- pkg install py39-loompy
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above. NOTE: This is a Python port. Instead of py39-loompy listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-loompy
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1646583060
SHA256 (loompy-3.0.7.tar.gz) = b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4
SIZE (loompy-3.0.7.tar.gz) = 4837617
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-click>0 : devel/py-click@py39
- py39-h5py>0 : science/py-h5py@py39
- py39-numba>0 : devel/py-numba@py39
- py39-numpy-groupies>0 : math/py-numpy-groupies@py39
- py39-pandas>0 : math/py-pandas@py39
- py39-scipy>0 : science/py-scipy@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/py-orange3-single-cell
Configuration Options:
- No options to configure
- Options name:
- biology_py-loompy
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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