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:

http://bioinf.uni-greifswald.de/augustus/

License:

Other / Artistic Licence

Recipe:

/augustus/meta.yaml

Links:

biotools: augustus, doi: 10.1093/bioinformatics/btr010, usegalaxy-eu: augustus

package augustus

versions:

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, 

3.5.0-3,  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,  3.3.3-12,  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:

>=2.5.1,<2.5.2.0a0

depends biopython:

depends boost-cpp:

>=1.78.0,<1.78.1.0a0

depends cdbtools:

depends diamond:

depends gsl:

>=2.7,<2.8.0a0

depends htslib:

>=1.17,<1.21.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libcblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends libsqlite:

>=3.41.2,<4.0a0

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

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 sqlite:

depends suitesparse:

>=5.10.1,<6.0a0

depends tar:

depends ucsc-fatotwobit:

depends ucsc-twobitinfo:

depends zlib:

requirements:

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 myenvname being 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.

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