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Port details
py-pyrodigal Python binding for Prodigal, an ORF finder for genomes and metagenomes
3.6.3 biology on this many watch lists=2 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 3.5.2Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
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).
HomepageHomepage    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:
  • ${PYTHON_PKGNAMEPREFIX}pyrodigal>0:biology/py-pyrodigal@${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>)
  • py311: py311-pyrodigal
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):
py39-pyrodigal
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly--2.2.0--3.2.13.2.13.2.1
FreeBSD:14:latest--2.0.3--2.1.0-2.1.0
FreeBSD:14:quarterly-----3.2.13.2.13.2.1
FreeBSD:15:latest--n/a-n/a3.2.23.2.23.2.2
 

py311-pyrodigal
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.6.33.6.3-3.6.33.6.3---
FreeBSD:13:quarterly3.5.23.5.2-3.5.23.5.2---
FreeBSD:14:latest3.5.23.6.3-3.5.23.6.3---
FreeBSD:14:quarterly3.5.23.5.2-3.5.23.5.2---
FreeBSD:15:latest3.6.33.6.3n/a3.6.3n/a---
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py311-cython3>0 : lang/cython3@py311
  2. py311-scikit-build-core>0 : devel/py-scikit-build-core@py311
  3. cmake : devel/cmake-core
  4. python3.11 : lang/python311
  5. py311-build>=0 : devel/py-build@py311
  6. py311-installer>=0 : devel/py-installer@py311
Test dependencies:
  1. py311-archspec>0 : devel/py-archspec@py311
  2. py311-pytest>=7,1 : devel/py-pytest@py311
  3. python3.11 : lang/python311
Runtime dependencies:
  1. 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:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/p/pyrodigal/
  2. https://pypi.org/packages/source/p/pyrodigal/
Collapse this list.

Number of commits found: 17

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.6.3
12 Nov 2024 08:32:35
commit hash: 7adb8c360bf587e65ba496fd9b7fc249ec795b10commit hash: 7adb8c360bf587e65ba496fd9b7fc249ec795b10commit hash: 7adb8c360bf587e65ba496fd9b7fc249ec795b10commit hash: 7adb8c360bf587e65ba496fd9b7fc249ec795b10 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.5.2 → 3.6.3
3.5.2
05 Sep 2024 08:48:51
commit hash: 66a68b0dffc37566a53c1489bf1df20520cf7e01commit hash: 66a68b0dffc37566a53c1489bf1df20520cf7e01commit hash: 66a68b0dffc37566a53c1489bf1df20520cf7e01commit hash: 66a68b0dffc37566a53c1489bf1df20520cf7e01 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.5.1 → 3.5.2

Reported by:	portscout
3.5.1
23 Jul 2024 00:34:23
commit hash: 46f1e266935d0f6c61a05d2f689641da68c88561commit hash: 46f1e266935d0f6c61a05d2f689641da68c88561commit hash: 46f1e266935d0f6c61a05d2f689641da68c88561commit hash: 46f1e266935d0f6c61a05d2f689641da68c88561 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.5.0 → 3.5.1

Reported by:	portscout
3.5.0
18 Jul 2024 08:22:46
commit hash: 38f9715debf8ec9b96f41e164b5fe2d6168084c2commit hash: 38f9715debf8ec9b96f41e164b5fe2d6168084c2commit hash: 38f9715debf8ec9b96f41e164b5fe2d6168084c2commit hash: 38f9715debf8ec9b96f41e164b5fe2d6168084c2 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.4.1 → 3.5.0

Reported by:	portscout
3.4.1
26 May 2024 17:51:27
commit hash: c5e70c355be25f2c803fdebbc8150e68b67e70a9commit hash: c5e70c355be25f2c803fdebbc8150e68b67e70a9commit hash: c5e70c355be25f2c803fdebbc8150e68b67e70a9commit hash: c5e70c355be25f2c803fdebbc8150e68b67e70a9 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
Author: Älven
biology/py-pyrodigal: update 3.4.0 → 3.4.1

PR:	279310
3.4.0
20 May 2024 05:18:25
commit hash: 1586be89c472e7c425fe5fad61089d03b424a501commit hash: 1586be89c472e7c425fe5fad61089d03b424a501commit hash: 1586be89c472e7c425fe5fad61089d03b424a501commit hash: 1586be89c472e7c425fe5fad61089d03b424a501 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.3.0 → 3.4.0

Reported by:	portscout
3.3.0
08 Mar 2024 22:34:40
commit hash: 8d3eb5c77ddc4739fd5901f8723aa4151eb14d75commit hash: 8d3eb5c77ddc4739fd5901f8723aa4151eb14d75commit hash: 8d3eb5c77ddc4739fd5901f8723aa4151eb14d75commit hash: 8d3eb5c77ddc4739fd5901f8723aa4151eb14d75 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.2.2 → 3.3.0

Reported by:	portscout
3.2.2
21 Jan 2024 09:44:54
commit hash: 9747b20f9aef29a87c32a5242bfe31f9adda1ec0commit hash: 9747b20f9aef29a87c32a5242bfe31f9adda1ec0commit hash: 9747b20f9aef29a87c32a5242bfe31f9adda1ec0commit hash: 9747b20f9aef29a87c32a5242bfe31f9adda1ec0 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.2.1 → 3.2.2

Reported by:	portscout
3.2.1
20 Dec 2023 07:02:18
commit hash: bbe4f4366ca5de591f49b53a0e6b92e8345e0fb0commit hash: bbe4f4366ca5de591f49b53a0e6b92e8345e0fb0commit hash: bbe4f4366ca5de591f49b53a0e6b92e8345e0fb0commit hash: bbe4f4366ca5de591f49b53a0e6b92e8345e0fb0 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.1.1 → 3.2.1

Reported by:	portscout
3.1.1
07 Nov 2023 17:56:52
commit hash: 2b9afc37187b488a6cd069773b34a94d022fb130commit hash: 2b9afc37187b488a6cd069773b34a94d022fb130commit hash: 2b9afc37187b488a6cd069773b34a94d022fb130commit hash: 2b9afc37187b488a6cd069773b34a94d022fb130 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 3.1.0 → 3.1.1

Reported by:	portscout
3.1.0
05 Nov 2023 23:07:54
commit hash: 682788bfb9fe00bbe6809f5f181960e9a0622a73commit hash: 682788bfb9fe00bbe6809f5f181960e9a0622a73commit hash: 682788bfb9fe00bbe6809f5f181960e9a0622a73commit hash: 682788bfb9fe00bbe6809f5f181960e9a0622a73 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: update 2.2.0 → 3.1.0

Reported by:	portscout
2.2.0
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
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
commit hash: c0e044bc3d5f6e9787b89ebf571a8324a6de8e73commit hash: c0e044bc3d5f6e9787b89ebf571a8324a6de8e73commit hash: c0e044bc3d5f6e9787b89ebf571a8324a6de8e73commit hash: c0e044bc3d5f6e9787b89ebf571a8324a6de8e73 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: Update 2.1.0 → 2.2.0

Reported by:	portscout
2.1.0
19 Mar 2023 16:42:53
commit hash: 9d07cf3ba24db7a5450946e7d4e20cd50bb43ea7commit hash: 9d07cf3ba24db7a5450946e7d4e20cd50bb43ea7commit hash: 9d07cf3ba24db7a5450946e7d4e20cd50bb43ea7commit hash: 9d07cf3ba24db7a5450946e7d4e20cd50bb43ea7 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: Update 2.0.3 → 2.1.0

Reported by:	portscout
2.0.3
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
2.0.3
22 Dec 2022 08:43:31
commit hash: ab183e22f0ddf760036e708b9786abf5724c411fcommit hash: ab183e22f0ddf760036e708b9786abf5724c411fcommit hash: ab183e22f0ddf760036e708b9786abf5724c411fcommit hash: ab183e22f0ddf760036e708b9786abf5724c411f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: Update 2.0.2 -> 2.0.3

Reported by:	portscout
2.0.2
06 Dec 2022 15:41:19
commit hash: 29c79a3b6aee93dbe5b65e863bcb33e1bb773276commit hash: 29c79a3b6aee93dbe5b65e863bcb33e1bb773276commit hash: 29c79a3b6aee93dbe5b65e863bcb33e1bb773276commit hash: 29c79a3b6aee93dbe5b65e863bcb33e1bb773276 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for
genomes and metagenomes

Number of commits found: 17