| Port details |
- prodigal Protein-coding gene prediction for prokaryotic genomes
- 2.6.3.16 biology
 =2      2.6.3.16Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-02-03 18:08:28
- Last Update: 2023-07-22 07:37:33
- Commit Hash: 39b34c7
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/hyattpd/Prodigal
- Description:
- Fast, reliable protein-coding gene prediction for prokaryotic genomes.
Features:
* Predicts protein-coding genes: Prodigal provides fast, accurate protein-coding
gene predictions in GFF3, Genbank, or Sequin table format.
* Handles draft genomes and metagenomes: Prodigal runs smoothly on finished
genomes, draft genomes, and metagenomes.
* Runs quickly: Prodigal analyzes the E. coli K-12 genome in 10 seconds on a
modern MacBook Pro.
* Runs unsupervised: Prodigal is an unsupervised machine learning algorithm. It
does not need to be provided with any training data, and instead automatically
learns the properties of the genome from the sequence itself, including RBS
motif usage, start codon usage, and coding statistics.
* Handles gaps and partial genes: The user can specify if Prodigal should build
genes across runs of N's as well as how to handle genes at the edges of
contigs.
* Identifies translation initiation sites: Prodigal predicts the correct
translation initiation site for most genes, and can output information about
every potential start site in the genome, including confidence score, RBS
motif, and much more.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- prodigal>0:biology/prodigal
- To install the port:
- cd /usr/ports/biology/prodigal/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/prodigal
- pkg install prodigal
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: prodigal
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1690009429
SHA256 (hyattpd-Prodigal-v2.6.3-16-gc1e2d36_GH0.tar.gz) = 8d12b956cc20e971f38df1b201765d5ee03356ada809ed39470bac62e9ae53f4
SIZE (hyattpd-Prodigal-v2.6.3-16-gc1e2d36_GH0.tar.gz) = 612591
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:
-
- gmake>=4.3 : devel/gmake
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_prodigal
- USES:
- gmake
- 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 |
|---|
2.6.3.16
22 Jul 2023 07:37:33
 |
Yuri Victorovich (yuri) |
biology/prodigal: Update 2.6.3-7 → 2.6.3-16 |
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) |
2.6.3.7
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  ) |
2.6.3.7
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.6.3.7
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.6.3.7
12 Oct 2019 15:40:21
 |
yuri |
biology/prodigal: Eliminate a very old version from the portscout discovery
process |
2.6.3.7
12 Oct 2019 15:36:47
|
yuri |
biology/prodigal: Update 2.6.3-2 -> 2.6.3-7 |
2.6.3.2
03 Feb 2019 18:08:14
|
yuri |
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic
genomes |
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