recipe metagem

Generate context specific genome-scale metabolic models and predict metabolic interactions directly from metagenomic data

Homepage:

https://github.com/franciscozorrilla/metaGEM

License:

MIT

Recipe:

/metagem/meta.yaml

Links:

doi: 10.1093/nar/gkab815, biotools: metagem

package metagem

Versions:

1.0.5-0

Depends:

• bedtools >=2.29.2

• bwa >=0.7.17

• concoct >=1.1.0

• diamond >=2.0.6

• fastp >=0.20.1

• gtdbtk >=1.4.0

• maxbin2 >=2.2.7

• megahit >=1.2.9

• metabat2 >=2.15

• python >=3.7

• r-base >=3.5.1

• r-gridextra >=2.2.1

• r-tidytext

• r-tidyverse

• samtools >=1.9

• snakemake >=5.10.0,<5.31.1

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install metagem

and update with:

conda update metagem

or use the docker container:

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

(see metagem/tags for valid values for <tag>)

Download stats

Link to this page

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