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-annotate-bins

(downloads) docker_metawrap-annotate-bins

versions:

1.3.0-3

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends prokka:

1.*

requirements:

additional platforms:

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-annotate-bins

and update with::

   mamba update metawrap-annotate-bins

To create a new environment, run:

mamba create --name myenvname metawrap-annotate-bins

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-annotate-bins:<tag>

(see `metawrap-annotate-bins/tags`_ for valid values for ``<tag>``)
package metawrap-assembly

(downloads) docker_metawrap-assembly

versions:

1.3.0-3

depends bowtie2:

2.3.5.*

depends bwa:

0.7.17.*

depends megahit:

1.1.3.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends quast:

5.0.2.*

depends spades:

3.13.0.*

requirements:

additional platforms:

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-assembly

and update with::

   mamba update metawrap-assembly

To create a new environment, run:

mamba create --name myenvname metawrap-assembly

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-assembly:<tag>

(see `metawrap-assembly/tags`_ for valid values for ``<tag>``)
package metawrap-binning

(downloads) docker_metawrap-binning

versions:

1.3.0-3

depends bwa:

0.7.17.*

depends checkm-genome:

1.0.12.*

depends concoct:

1.0.0.*

depends curl:

depends libgfortran:

3.*

depends maxbin2:

2.2.6.*

depends metabat2:

2.12.1.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends pplacer:

1.1.alpha19.*

depends samtools:

1.9.*

requirements:

additional platforms:

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-binning

and update with::

   mamba update metawrap-binning

To create a new environment, run:

mamba create --name myenvname metawrap-binning

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-binning:<tag>

(see `metawrap-binning/tags`_ for valid values for ``<tag>``)
package metawrap-blobology

(downloads) docker_metawrap-blobology

versions:

1.3.0-3

depends blast:

2.6.0.*

depends bowtie2:

2.3.5.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends perl-bioperl:

depends r-ggplot2:

3.1.0.*

depends r-recommended:

3.5.1.*

depends r-reshape2:

depends samtools:

1.9.*

requirements:

additional platforms:

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-blobology

and update with::

   mamba update metawrap-blobology

To create a new environment, run:

mamba create --name myenvname metawrap-blobology

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-blobology:<tag>

(see `metawrap-blobology/tags`_ for valid values for ``<tag>``)
package metawrap-classify-bins

(downloads) docker_metawrap-classify-bins

versions:

1.3.0-3

depends blast:

2.6.0.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends taxator-tk:

1.3.3e.*

requirements:

additional platforms:

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-classify-bins

and update with::

   mamba update metawrap-classify-bins

To create a new environment, run:

mamba create --name myenvname metawrap-classify-bins

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-classify-bins:<tag>

(see `metawrap-classify-bins/tags`_ for valid values for ``<tag>``)
package metawrap-kraken

(downloads) docker_metawrap-kraken

versions:

1.3.0-3

depends jellyfish:

depends kraken:

1.1.1.*

depends kraken2:

2.0.*

depends krona:

2.7.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

requirements:

additional platforms:

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-kraken

and update with::

   mamba update metawrap-kraken

To create a new environment, run:

mamba create --name myenvname metawrap-kraken

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-kraken:<tag>

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

(downloads) docker_metawrap-mg

versions:

1.3.0-3,  1.3.0-1,  1.3.0-0

depends biopython:

1.72.*

depends python:

2.7.15.*

requirements:

additional platforms:

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>``)
package metawrap-quant-bins

(downloads) docker_metawrap-quant-bins

versions:

1.3.0-3

depends matplotlib-base:

2.2.5.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends pandas:

0.24.2.*

depends salmon:

0.15.0.*

depends seaborn:

0.9.0.*

requirements:

additional platforms:

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-quant-bins

and update with::

   mamba update metawrap-quant-bins

To create a new environment, run:

mamba create --name myenvname metawrap-quant-bins

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-quant-bins:<tag>

(see `metawrap-quant-bins/tags`_ for valid values for ``<tag>``)
package metawrap-read-qc

(downloads) docker_metawrap-read-qc

versions:

1.3.0-3

depends bmtagger:

3.101.*

depends fastqc:

0.11.8.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends trim-galore:

0.5.0.*

requirements:

additional platforms:

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-read-qc

and update with::

   mamba update metawrap-read-qc

To create a new environment, run:

mamba create --name myenvname metawrap-read-qc

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-read-qc:<tag>

(see `metawrap-read-qc/tags`_ for valid values for ``<tag>``)
package metawrap-reassemble-bins

(downloads) docker_metawrap-reassemble-bins

versions:

1.3.0-3

depends bwa:

0.7.17.*

depends checkm-genome:

1.0.12.*

depends curl:

depends matplotlib-base:

2.2.5.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends minimap2:

depends pplacer:

1.1.alpha19.*

depends spades:

3.13.0.*

requirements:

additional platforms:

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-reassemble-bins

and update with::

   mamba update metawrap-reassemble-bins

To create a new environment, run:

mamba create --name myenvname metawrap-reassemble-bins

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-reassemble-bins:<tag>

(see `metawrap-reassemble-bins/tags`_ for valid values for ``<tag>``)
package metawrap-refinement

(downloads) docker_metawrap-refinement

versions:

1.3.0-3

depends checkm-genome:

1.0.12.*

depends curl:

depends jellyfish:

depends kraken:

1.1.1.*

depends krona:

2.7.*

depends matplotlib-base:

2.2.5.*

depends metawrap-mg:

>=1.3.0,<1.4.0a0

depends pplacer:

1.1.alpha19.*

requirements:

additional platforms:

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-refinement

and update with::

   mamba update metawrap-refinement

To create a new environment, run:

mamba create --name myenvname metawrap-refinement

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-refinement:<tag>

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

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