recipe metawrap-mg

MetaWRAP is a pipeline for genome-resolved metagenomic data analysis

Homepage:

https://github.com/bxlab/metaWRAP

License:

MIT

Recipe:

/metawrap-mg/meta.yaml

package metawrap-mg

(downloads) docker_metawrap-mg

versions:

1.3.0-1,  1.3.0-0

depends biopython:

1.68.*

depends blas:

2.5 mkl

depends blast:

2.6.0.*

depends bmtagger:

3.101.*

depends bowtie2:

2.3.5.*

depends bwa:

0.7.17.*

depends checkm-genome:

1.0.12.*

depends concoct:

1.0.0.*

depends fastqc:

0.11.8.*

depends kraken:

1.1.*

depends kraken2:

2.0.*

depends krona:

2.7.*

depends matplotlib-base:

2.2.3.*

depends maxbin2:

2.2.6.*

depends megahit:

1.1.3.*

depends metabat2:

2.12.1.*

depends openssl:

1.0.*

depends pandas:

0.24.2.*

depends perl-bioperl:

depends pplacer:

1.1.alpha19.*

depends prokka:

1.*

depends python:

2.7.15.*

depends quast:

5.0.2.*

depends r-ggplot2:

3.1.0.*

depends r-recommended:

3.5.1.*

depends r-reshape2:

depends salmon:

0.13.1.*

depends samtools:

1.9.*

depends seaborn:

0.9.0.*

depends spades:

3.13.0.*

depends taxator-tk:

1.3.3e.*

depends trim-galore:

0.5.0.*

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 metawrap-mg

and update with::

   mamba update metawrap-mg

To create a new environment, run:

mamba create --name myenvname metawrap-mg

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/metawrap-mg:<tag>

(see `metawrap-mg/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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