recipe das_tool

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Homepage:

https://github.com/cmks/DAS_Tool

License:

BSD

Recipe:

/das_tool/meta.yaml

Links:

doi: 10.1038/s41564-018-0171-1

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

package das_tool

(downloads) docker_das_tool

Versions:
1.1.7-1,  1.1.7-0,  1.1.6-0,  1.1.5-0,  1.1.4-1,  1.1.4-0,  1.1.3-0,  1.1.2-2,  1.1.2-1, 

1.1.7-1,  1.1.7-0,  1.1.6-0,  1.1.5-0,  1.1.4-1,  1.1.4-0,  1.1.3-0,  1.1.2-2,  1.1.2-1,  1.1.2-0,  1.1.1-3,  1.1.1-2,  1.1.1-1,  1.1.1-0

Depends:

  • on blast >=2.7.1

  • on diamond >=0.9.14

  • on gawk

  • on prodigal >=2.6.3

  • on pullseq >=1.0.2

  • on r-base >=4.4,<4.5.0a0

  • on r-data.table >=1.9.6

  • on r-docopt >=0.7.1

  • on r-magrittr >=2.0.1

  • on ruby >=2.4.4

  • on unzip

Additional platforms:

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 das_tool

to add into an existing workspace instead, run:

pixi add das_tool

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 das_tool

Alternatively, to install into a new environment, run:

conda create -n envname das_tool

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/das_tool:<tag>

(see das_tool/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.

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