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Port details
py-ont-fast5-api Interface to HDF5 files in Oxford Nanopore .fast5 format
4.0.2_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 4.0.2_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-13 13:36:06
Last Update: 2023-04-23 09:09:58
Commit Hash: 8d3e020
Also Listed In: python
License: MPL20
WWW:
https://pypi.python.org/pypi/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
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

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 py39-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 py39-ont-fast5-api listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-ont-fast5-api
Package flavors (<flavor>: <package>)
  • py39: py39-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):
py39-ont-fast5-api
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest4.0.2_14.0.2_1-4.0.2_14.0.2_1---
FreeBSD:13:quarterly4.0.2_14.0.2_1-4.0.2_14.0.2_1---
FreeBSD:14:latest4.0.2_14.0.2_1-4.0.2_14.0.2_1---
FreeBSD:14:quarterly4.0.2_14.0.2_1-4.0.2_14.0.2_1---
FreeBSD:15:latest4.0.2_14.0.2_1n/a-n/a--4.0.2_1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  2. python3.9 : lang/python39
Test dependencies:
  1. py39-pip>=0 : devel/py-pip@py39
  2. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
  2. py39-h5py>=2.2.0 : science/py-h5py@py39
  3. py39-six>0 : devel/py-six@py39
  4. py39-progressbar>0 : misc/py-progressbar@py39
  5. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  6. python3.9 : lang/python39
Library dependencies:
  1. libvbz_hdf_plugin.so : archivers/vbz-compression
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/nanoporetech/ont_fast5_api/tar.gz/release_4.0.2?dummy=/
Collapse this list.

Number of commits found: 5

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
4.0.2_1
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
4.0.2
25 Mar 2022 16:37:29
commit hash: fad5d1754c6cacc578077dfa752196f3db3271f7commit hash: fad5d1754c6cacc578077dfa752196f3db3271f7commit hash: fad5d1754c6cacc578077dfa752196f3db3271f7commit hash: fad5d1754c6cacc578077dfa752196f3db3271f7 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 5797d6a3298ebfe3990db73084f34ed935911efacommit hash: 5797d6a3298ebfe3990db73084f34ed935911efacommit hash: 5797d6a3298ebfe3990db73084f34ed935911efacommit hash: 5797d6a3298ebfe3990db73084f34ed935911efa files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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: 5