Port details on branch 2022Q2 |
- augustus Genome annotation tool
- 3.5.0_8 biology =0 3.5.0_5Version of this port present on the latest quarterly branch.
- Maintainer: yuri@FreeBSD.org
- Port Added: 2022-11-25 23:57:41
- Last Update: 2024-01-28 12:02:23
- Commit Hash: 68a7254
- 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>=4.3 : devel/gmake
- python3.9 : lang/python39
- perl5>=5.36<5.37 : lang/perl5.36
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- samtools : biology/samtools
- python3.9 : lang/python39
- 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:
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