BSD Portsbiology/py-ont-fast5-api 4.1.3 FreeBSD
Interface to HDF5 files in Oxford Nanopore .fast5 format
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MPL20
- Categories
- biology, python
Description
The ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. It provides:
o Implementation of the fast5 file schema using h5py library
o Methods to interact with and reflect the fast5 file schema
o Tools to convert between multi\_read and single\_read formats
o Tools to compress/decompress raw data in files
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/py-ont-fast5-api | 4.1.3 |
| DragonFly | biology/py-ont-fast5-api | 4.0.2_1 |
| HardenedBSD | biology/py-ont-fast5-api | 4.1.3 |
| GhostBSD | biology/py-ont-fast5-api | 4.1.3 |
Install
Binary package:
pkg install py312-ont-fast5-apiFrom the ports tree:
cd /usr/ports/biology/py-ont-fast5-api/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= py312-ont-fast5-api>0:biology/py-ont-fast5-apiPackages
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 | - | 4.1.3 | - | 4.0.2_2 | 4.1.3 |
| FreeBSD:14:quarterly | - | 4.1.3 | n/a | 4.0.2_2 | 4.1.3 |
| FreeBSD:15:latest | - | 4.1.3 | n/a | 4.0.2_2 | 4.0.2_2 |
| FreeBSD:15:quarterly | - | 4.1.3 | n/a | n/a | n/a |
| FreeBSD:16:latest | - | 4.1.3 | 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.
Library 1
libvbz_hdf_plugin.so: archivers/vbz-compression
Runtime 3
${PYTHON_PKGNAMEPREFIX}h5py>=3: science/py-h5py${PYTHON_PKGNAMEPREFIX}packaging>0: devel/py-packaging${PYTHON_PKGNAMEPREFIX}progressbar>=2.3.1: misc/py-progressbar
Test 1
${PYTHON_PKGNAMEPREFIX}pip>=0: devel/py-pip
The full lists below include those, and their dependencies in turn.
Build dependencies 19
Run dependencies 23
- archivers/liblz4
- archivers/vbz-compression
- archivers/zstd
- devel/binutils
- devel/gettext-runtime
- devel/libffi
- devel/py-packaging
- devel/readline
- lang/gcc14
- lang/python312
- lang/python315
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-numpy
- misc/py-progressbar
- print/indexinfo
- science/hdf5
- science/libaec
- science/py-h5py
- textproc/expat2
Required by 1
Configuration
No options to configure.
- USES
- python
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| nanoporetech-ont_fast5_api-release_4.1.3_GH0.tar.gz | 4.443485e+06 | 80e021a6fbb1c442d0d782ca36815e4cc653bd352431489995285e96fb98d96c |