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Port details
py-pyrodigal Python binding for Prodigal, an ORF finder for genomes and metagenomes
3.4.0 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 3.3.0Version 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: 2024-05-20 05:18:25
Commit Hash: 1586be8
Also Listed In: python
License: GPLv3
WWW:
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).
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:
  • ${PYTHON_PKGNAMEPREFIX}pyrodigal>0:biology/py-pyrodigal@${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 py39-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 py39-pyrodigal listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-pyrodigal
Package flavors (<flavor>: <package>)
  • py39: py39-pyrodigal
distinfo:
TIMESTAMP = 1716179060 SHA256 (pyrodigal-3.4.0.tar.gz) = d4714e8f9208b7768f89bca9f47013e9f18f978e4baf43176a67af9cb26c7c79 SIZE (pyrodigal-3.4.0.tar.gz) = 2577063

Packages (timestamps in pop-ups are UTC):
py39-pyrodigal
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.3.03.4.0-3.3.03.4.0---
FreeBSD:13:quarterly3.3.03.3.02.2.03.3.03.3.03.2.13.2.13.2.1
FreeBSD:14:latest3.3.03.3.02.0.33.3.03.4.02.1.0-2.1.0
FreeBSD:14:quarterly3.3.03.3.0-3.3.03.3.03.2.13.2.13.2.1
FreeBSD:15:latest3.3.03.4.0n/a3.3.0n/a3.2.23.2.23.2.2
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-cython3>0 : lang/cython3@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
Test dependencies:
  1. py39-archspec>0 : devel/py-archspec@py39
  2. py39-pytest>=7,1 : devel/py-pytest@py39
  3. python3.9 : lang/python39
Runtime dependencies:
  1. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  2. python3.9 : lang/python39
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_py-pyrodigal
USES:
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: 12

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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: 12