Package Recipe 'augustus'

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:: https://bioinf.uni-greifswald.de/augustus
Documentation:: https://github.com/Gaius-Augustus/Augustus/blob/v3.5.0/docs/RUNNING-AUGUSTUS.md
Developer docs:: https://github.com/Gaius-Augustus/Augustus
License:: Other / Artistic License
Recipe:: /augustus/meta.yaml
Links:: biotools: augustus, usegalaxy-eu: augustus, usegalaxy-eu: augustus_training, doi: 10.1093/bioinformatics/btr010, usegalaxy-eu: augustus, usegalaxy-eu: augustus_training

package augustus¶

Versions:

3.5.0-9, 3.5.0-8, 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,

3.5.0-9, 3.5.0-8, 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:

on bamtools >=2.5.3,<3.0a0
on biopython
on boost-cpp
on cdbtools
on diamond
on gsl >=2.8
on gsl >=2.8,<2.9.0a0
on htslib >=1.22.1,<1.23.0a0
on libamd >=3.3.3,<4.0a0
on libblas >=3.9.0,<4.0a0
on libbtf >=2.3.2,<3.0a0
on libcamd >=3.3.3,<4.0a0
on libcblas >=3.9.0,<4.0a0
on libccolamd >=3.3.4,<4.0a0
on libcholmod >=5.3.1,<6.0a0
on libcolamd >=3.3.4,<4.0a0
on libcxsparse >=4.4.1,<5.0a0
on libgcc >=13
on libklu >=2.3.5,<3.0a0
on libldl >=3.3.2,<4.0a0
on libparu >=1.0.0,<2.0a0
on librbio >=4.3.4,<5.0a0
on libspex >=3.2.3,<4.0a0
on libspqr >=4.3.4,<5.0a0
on libsqlite >=3.50.4,<4.0a0
on libstdcxx >=13
on libsuitesparseconfig >=7.10.1,<8.0a0
on libumfpack >=6.3.5,<7.0a0
on libzlib >=1.3.1,<2.0a0
on lp_solve
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-app-cpanminus
on perl-dbi
on perl-file-which
on perl-module-build 0.4234.*
on perl-parallel-forkmanager
on perl-scalar-list-utils
on perl-yaml
on samtools >=1.22.1,<2.0a0
on sqlite
on suitesparse >=7.10.1,<8.0a0
on tar
on ucsc-fatotwobit
on ucsc-twobitinfo

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install augustus

to add into an existing workspace instead, run:

pixi add augustus

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install augustus

Alternatively, to install into a new environment, run:

conda create -n envname augustus

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/augustus:<tag>

(see augustus/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augustus/README.html)