| Port details |
- py-pyrodigal Python binding for Prodigal, an ORF finder for genomes and metagenomes
- 3.6.3 biology
 =2      3.5.2Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2022-12-06 17:27:05
- Last Update: 2024-11-12 08:32:35
- Commit Hash: 7adb8c36
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: GPLv3
- WWW:
- https://pyrodigal.readthedocs.io/en/stable/
- https://github.com/althonos/pyrodigal/
- Description:
- Pyrodigal is a Python module that provides bindings to Prodigal using Cython.
Features:
The library now features everything from the original Prodigal CLI:
* run mode selection: Choose between single mode, using a training sequence
to count nucleotide hexamers, or metagenomic mode, using pre-trained data
from different organisms (prodigal -p).
* region masking: Prevent genes from being predicted across regions
containing unknown nucleotides (prodigal -m).
* closed ends: Genes will be identified as running over edges if they are
larger than a certain size, but this can be disabled (prodigal -c).
* training configuration: During the training process, a custom translation
table can be given (prodigal -g), and the Shine-Dalgarno motif search can
be forcefully bypassed (prodigal -n)
* output files: Output files can be written in a format mostly compatible
with the Prodigal binary, including the protein translations in FASTA
format (prodigal -a), the gene sequences in FASTA format (prodigal -d),
or the potential gene scores in tabular format (prodigal -s).
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}pyrodigal>0:biology/py-pyrodigal@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-pyrodigal/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-pyrodigal
- pkg install py311-pyrodigal
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-pyrodigal listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-pyrodigal
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1731398873
SHA256 (pyrodigal-3.6.3.tar.gz) = 3e226f743c960d4d30c46ae6868aff7e2a6b98f8d837cfbd2637568569b21f78
SIZE (pyrodigal-3.6.3.tar.gz) = 3589356
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-cython3>0 : lang/cython3@py311
- py311-scikit-build-core>0 : devel/py-scikit-build-core@py311
- cmake : devel/cmake-core
- python3.11 : lang/python311
- py311-build>=0 : devel/py-build@py311
- py311-installer>=0 : devel/py-installer@py311
- Test dependencies:
-
- py311-archspec>0 : devel/py-archspec@py311
- py311-pytest>=7,1 : devel/py-pytest@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- python3.11 : lang/python311
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-pyrodigal
- USES:
- cmake:indirect python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
3.6.3
12 Nov 2024 08:32:35
 |
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.5.2 → 3.6.3 |
3.5.2
05 Sep 2024 08:48:51
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.5.1 → 3.5.2
Reported by: portscout |
3.5.1
23 Jul 2024 00:34:23
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.5.0 → 3.5.1
Reported by: portscout |
3.5.0
18 Jul 2024 08:22:46
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.4.1 → 3.5.0
Reported by: portscout |
3.4.1
26 May 2024 17:51:27
|
Yuri Victorovich (yuri)
Author: Älven |
biology/py-pyrodigal: update 3.4.0 → 3.4.1
PR: 279310 |
3.4.0
20 May 2024 05:18:25
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.3.0 → 3.4.0
Reported by: portscout |
3.3.0
08 Mar 2024 22:34:40
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.2.2 → 3.3.0
Reported by: portscout |
3.2.2
21 Jan 2024 09:44:54
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.2.1 → 3.2.2
Reported by: portscout |
3.2.1
20 Dec 2023 07:02:18
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.1.1 → 3.2.1
Reported by: portscout |
3.1.1
07 Nov 2023 17:56:52
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 3.1.0 → 3.1.1
Reported by: portscout |
3.1.0
05 Nov 2023 23:07:54
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: update 2.2.0 → 3.1.0
Reported by: portscout |
2.2.0
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
2.2.0
26 Jun 2023 17:01:59
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: Update 2.1.0 → 2.2.0
Reported by: portscout |
2.1.0
19 Mar 2023 16:42:53
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: Update 2.0.3 → 2.1.0
Reported by: portscout |
2.0.3
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
2.0.3
22 Dec 2022 08:43:31
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: Update 2.0.2 -> 2.0.3
Reported by: portscout |
2.0.2
06 Dec 2022 15:41:19
|
Yuri Victorovich (yuri) |
biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for
genomes and metagenomes |
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