| Port details |
- augustus Genome annotation tool
- 3.5.0_11 biology
 =2      3.5.0_9Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2022-11-25 23:57:41
- Last Update: 2024-11-20 10:05:25
- Commit Hash: 312ee18
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: science
- License: GPLv3
- WWW:
- http://bioinf.uni-greifswald.de/webaugustus/
- Description:
- AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
AUGUSTUS usually belongs to the most accurate programs for the species it is
trained for. Often it is the most accurate ab initio program. For example, at
the independent gene finder assessment (EGASP) on the human ENCODE regions
AUGUSTUS was the most accurate gene finder among the tested ab initio programs.
At the more recent nGASP (worm), it was among the best in the ab initio and
transcript-based categories. See accuracy statistics for further details.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- augustus-gene-prediction>0:biology/augustus
- To install the port:
- cd /usr/ports/biology/augustus/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/augustus
- pkg install augustus-gene-prediction
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: augustus-gene-prediction
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1669409399
SHA256 (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686
SIZE (Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz) = 225918930
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>=4.4.1 : devel/gmake
- python3.11 : lang/python311
- perl5>=5.36<5.37 : lang/perl5.36
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- samtools : biology/samtools
- python3.11 : lang/python311
- perl5>=5.36<5.37 : lang/perl5.36
- Library dependencies:
-
- libbamtools.so : biology/bamtools
- libboost_iostreams.so : devel/boost-libs
- libcolamd.so : math/suitesparse-colamd
- libgsl.so : math/gsl
- libhts.so : biology/htslib
- liblpsolve55.so : math/lp_solve
- libmysqlpp.so : databases/mysql++
- libmysqlclient.so.21 : databases/mysql80-client
- libsqlite3.so : databases/sqlite3
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_augustus
- USES:
- gmake localbase:ldflags mysql perl5 python sqlite shebangfix
- 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 |
|---|
3.5.0_11
20 Nov 2024 10:05:25
 |
Dima Panov (fluffy) |
devel/boost: bump consu,ers after update Boost to 1.86 release
Sponsored by: Future Crew, LLC |
3.5.0_10
03 Oct 2024 10:25:14
|
Dima Panov (fluffy) |
*/*: bump consumers after devel/boost* update
With hat: office
Sponsored by: Future Crew, LLC |
3.5.0_9
29 Apr 2024 20:08:56
|
Thierry Thomas (thierry) |
*/*: chase SuiteSparse’s upgrade |
3.5.0_8
28 Jan 2024 12:02:23
|
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade to SuiteSparse |
3.5.0_7
13 Jan 2024 10:19:22
|
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0 |
3.5.0_6
31 Dec 2023 14:31:11
|
Thierry Thomas (thierry) |
*/*: chase the upgrade of SuiteSparse |
3.5.0_5
15 Oct 2023 09:03:17
|
Thierry Thomas (thierry) |
*/*: chase the upgrade of SuiteSparse |
3.5.0_4
20 Sep 2023 17:57:40
|
Thierry Thomas (thierry) |
/*: bump PORTREVISION after the upgrade of SuiteSparse |
3.5.0_3
06 Aug 2023 21:53:03
|
Muhammad Moinur Rahman (bofh) |
biology/augustus: Fix build with llvm16
Approved by: portmgr (blanket)
Sponsored by: The FreeBSD Foundation |
3.5.0_3
01 Jul 2023 16:11:11
|
Thierry Thomas (thierry) |
*/*: bump PORTREVISION after the upgrade of SuiteSparse |
3.5.0_2
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
3.5.0_1
19 Jan 2023 16:45:37
|
Thierry Thomas (thierry) |
math/suitesparse*: bump PORTREVISION of dependant ports |
3.5.0
25 Nov 2022 23:55:09
|
Yuri Victorovich (yuri) |
biology/augustus: New port: Genome annotation tool |
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