| Port details |
- py-ont-fast5-api Interface to HDF5 files in Oxford Nanopore .fast5 format
- 4.0.2_1 biology
 =2      4.0.2_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-08-13 13:36:06
- Last Update: 2025-02-21 13:04:08
- Commit Hash: d758b1c
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: MPL20
- WWW:
- https://github.com/nanoporetech/ont_fast5_api/
- 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
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-ont-fast5-api/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-ont-fast5-api
- pkg install py311-ont-fast5-api
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 py311-ont-fast5-api listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-ont-fast5-api
- Package flavors (<flavor>: <package>)
- py311: py311-ont-fast5-api
- distinfo:
- TIMESTAMP = 1648128656
SHA256 (nanoporetech-ont_fast5_api-release_4.0.2_GH0.tar.gz) = c078dc0d20b02cd9807105415f259e099f1adc8b922d67a1a9fe04321c098361
SIZE (nanoporetech-ont_fast5_api-release_4.0.2_GH0.tar.gz) = 4082466
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:
-
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Test dependencies:
-
- py311-pip>=0 : devel/py-pip@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-h5py>=2.2.0 : science/py-h5py@py311
- py311-six>0 : devel/py-six@py311
- py311-progressbar>0 : misc/py-progressbar@py311
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Library dependencies:
-
- libvbz_hdf_plugin.so : archivers/vbz-compression
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_py-ont-fast5-api
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 6
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
4.0.2_1
21 Feb 2025 13:04:08
 |
Jason W. Bacon (jwb) |
Multiple biology ports: Replace pypi homepage with github
portscout apparently can't work with PYPI homepages |
4.0.2_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
4.0.2
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
4.0.2
25 Mar 2022 16:37:29
|
Jason W. Bacon (jwb) |
biology/py-ont-fast5-api: Update to 4.0.2
Minor bug fix release
Also disabled install of test directory, which was not properly
installed under the package subdir and caused a conflict as a result
PR: 262759 |
4.0.0
13 Aug 2021 13:34:09
|
Jason W. Bacon (jwb) |
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
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 |
Number of commits found: 6
|
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