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

3.4.0-2,  3.4.0-1,  3.4.0-0,  3.3.3-6,  3.3.3-5,  3.3.3-4,  3.3.3-3,  3.3.3-2,  3.3.3-1, 

3.4.0-2,  3.4.0-1,  3.4.0-0,  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

• biopython

• boost-cpp >=1.74.0,<1.74.1.0a0

• cdbtools

• diamond

• gsl >=2.6,<2.7.0a0

• htslib >=1.12,<1.13.0a0

• libblas >=3.8.0,<4.0a0

• libcblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• libstdcxx-ng >=9.3.0

• lp_solve

• perl >=5.26.2,<5.26.3.0a0

• perl-app-cpanminus

• perl-dbi

• perl-file-which

• perl-module-build

• perl-parallel-forkmanager

• perl-scalar-list-utils

• perl-yaml

• sqlite >=3.36.0,<4.0a0

• suitesparse >=5.10.1,<6.0a0

• tar

• ucsc-fatotwobit

• ucsc-twobitinfo

• zlib >=1.2.11,<1.3.0a0

Required By

• busco

• maker

• braker2

• fgmp

• funannotate

• comparative-annotation-toolkit

• makehub

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install augustus

and update with:

conda update augustus

or 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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