BSD Portsbiology/py-loompy 3.0.8 FreeBSD
Work with .loom files for single-cell RNA-seq data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- BSD2CLAUSE
- Categories
- biology, python
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
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/py-loompy | 3.0.8 |
| HardenedBSD | biology/py-loompy | 3.0.8 |
Install
Binary package:
pkg install py312-loompyFrom the ports tree:
cd /usr/ports/biology/py-loompy/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= py312-loompy>0:biology/py-loompyPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | - | 3.0.8 | - | - | 3.0.8 |
| FreeBSD:14:quarterly | - | 3.0.8 | n/a | - | 3.0.8 |
| FreeBSD:15:latest | - | 3.0.8 | n/a | - | 3.0.7_2 |
| FreeBSD:15:quarterly | - | 3.0.8 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 3.0.8 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 1
${PYTHON_PKGNAMEPREFIX}wheel>0: devel/py-wheel
Runtime 6
${PYTHON_PKGNAMEPREFIX}click>0: devel/py-click${PYTHON_PKGNAMEPREFIX}h5py>0: science/py-h5py${PYTHON_PKGNAMEPREFIX}numba>0: devel/py-numba${PYTHON_PKGNAMEPREFIX}numpy>=1.16: math/py-numpy${PYTHON_PKGNAMEPREFIX}numpy-groupies>0: math/py-numpy-groupies${PYTHON_PKGNAMEPREFIX}scipy>0: science/py-scipy
The full lists below include those, and their dependencies in turn.
Build dependencies 16
Run dependencies 32
- archivers/liblz4
- archivers/zstd
- devel/binutils
- devel/gettext-runtime
- devel/hwloc2
- devel/level-zero
- devel/libffi
- devel/libpciaccess
- devel/llvm22
- devel/onetbb
- devel/py-click
- devel/py-llvmlite
- devel/py-numba
- devel/readline
- lang/gcc14
- lang/python312
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-numpy
- math/py-numpy-groupies
- math/qhull
- misc/hwdata
- print/indexinfo
- science/hdf5
- science/libaec
- science/py-h5py
- science/py-scipy
- textproc/expat2
- textproc/libxml2
No port depends on this one.
Configuration
No options to configure.
- USES
- python
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| loompy-3.0.8.tar.gz | 49618 | c1f48d0bf21aa2bbdeee21a0577553cba9609d9435d7c32b687686bbb5869ca7 |
Master sites 1
- PYPI
Commit history 0
No commits in the history this site was built from.