- recipe augustus
AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
- Homepage:
- Documentation:
https://github.com/Gaius-Augustus/Augustus/blob/v3.5.0/docs/RUNNING-AUGUSTUS.md
- Developer docs:
- License:
Other / Artistic Licence
- Recipe:
- Links:
biotools: augustus, doi: 10.1093/bioinformatics/btr010, usegalaxy-eu: augustus, usegalaxy-eu: augustus_training
- package augustus¶
- versions:
3.5.0-7,3.5.0-5,3.5.0-4,3.5.0-3,3.5.0-2,3.5.0-1,3.5.0-0,3.4.0-8,3.4.0-7,3.5.0-7,3.5.0-5,3.5.0-4,3.5.0-3,3.5.0-2,3.5.0-1,3.5.0-0,3.4.0-8,3.4.0-7,3.4.0-6,3.4.0-5,3.4.0-4,3.4.0-3,3.4.0-2,3.4.0-1,3.4.0-0,3.3.3-13,3.3.3-12,3.3.3-11,3.3.3-10,3.3.3-9,3.3.3-8,3.3.3-7,3.3.3-6,3.3.3-5,3.3.3-4,3.3.3-3,3.3.3-2,3.3.3-1,3.3.3-0,3.3.2-2,3.3.2-1,3.3.2-0,3.3-5,3.3-4,3.3-2,3.3-1,3.3-0,3.2.3-5,3.2.3-4,3.2.3-3,3.2.3-2,3.2.3-1,3.2.3-0,3.2.2-3,3.2.2-2,3.2.2-1,3.2.2-0,3.1-0- depends bamtools:
>=2.5.2,<2.6.0a0- depends biopython:
- depends boost-cpp:
- depends cdbtools:
- depends diamond:
- depends gsl:
>=2.7,<2.8.0a0- depends htslib:
>=1.21,<1.23.0a0- depends libamd:
>=3.3.3,<4.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libbtf:
>=2.3.2,<3.0a0- depends libcamd:
>=3.3.3,<4.0a0- depends libcblas:
>=3.9.0,<4.0a0- depends libccolamd:
>=3.3.4,<4.0a0- depends libcholmod:
>=5.3.1,<6.0a0- depends libcolamd:
>=3.3.4,<4.0a0- depends libcxsparse:
>=4.4.1,<5.0a0- depends libgcc:
- depends libgcc-ng:
>=12- depends libklu:
>=2.3.5,<3.0a0- depends libldl:
>=3.3.2,<4.0a0- depends libparu:
>=1.0.0,<2.0a0- depends librbio:
>=4.3.4,<5.0a0- depends libspex:
>=3.2.3,<4.0a0- depends libspqr:
>=4.3.4,<5.0a0- depends libsqlite:
>=3.49.1,<4.0a0- depends libstdcxx:
- depends libstdcxx-ng:
>=12- depends libsuitesparseconfig:
>=7.10.1,<8.0a0- depends libumfpack:
>=6.3.5,<7.0a0- depends libzlib:
>=1.3.1,<2.0a0- depends lp_solve:
- depends perl:
>=5.32.1,<5.33.0a0 *_perl5- depends perl-app-cpanminus:
- depends perl-dbi:
- depends perl-file-which:
- depends perl-module-build:
0.4234.*- depends perl-parallel-forkmanager:
- depends perl-scalar-list-utils:
- depends perl-yaml:
- depends samtools:
>=1.21,<2.0a0- depends sqlite:
- depends suitesparse:
>=7.10.1,<8.0a0- depends tar:
- depends ucsc-fatotwobit:
- depends ucsc-twobitinfo:
- requirements:
- additional platforms:
linux-aarch64
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install augustus and update with:: mamba update augustus
To create a new environment, run:
mamba create --name myenvname augustus
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/augustus:<tag> (see `augustus/tags`_ for valid values for ``<tag>``)
Notes¶
Builds with sqlite support are currently only available on Linux due to compile issues with macOS.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/augustus/README.html)
