Package Recipe 'metawrap-mg' — Bioconda documentation

recipe metawrap-mg

MetaWRAP is a pipeline for genome-resolved metagenomic data analysis

Homepage:: bxlab/metaWRAP
License:: MIT
Recipe:: /metawrap-mg/meta.yaml

package metawrap-annotate-bins#

Versions:

1.3.0-3

Depends:

on metawrap-mg >=1.3.0,<1.4.0a0
on prokka 1.*

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 metawrap-annotate-bins

to add into an existing workspace instead, run:

pixi add metawrap-annotate-bins

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 metawrap-annotate-bins

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-annotate-bins

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/metawrap-annotate-bins:<tag>

(see metawrap-annotate-bins/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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package metawrap-assembly#

Versions:

1.3.0-3

Depends:

on bowtie2 2.3.5.*
on bwa 0.7.17.*
on megahit 1.1.3.*
on metawrap-mg >=1.3.0,<1.4.0a0
on quast 5.0.2.*
on spades 3.13.0.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-assembly

to add into an existing workspace instead, run:

pixi add metawrap-assembly

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 metawrap-assembly

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-assembly

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/metawrap-assembly:<tag>

(see metawrap-assembly/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-binning#

Versions:

1.3.0-3

Depends:

on bwa 0.7.17.*
on checkm-genome 1.0.12.*
on concoct 1.0.0.*
on curl
on libgfortran 3.*
on maxbin2 2.2.6.*
on metabat2 2.12.1.*
on metawrap-mg >=1.3.0,<1.4.0a0
on pplacer 1.1.alpha19.*
on samtools 1.9.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-binning

to add into an existing workspace instead, run:

pixi add metawrap-binning

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 metawrap-binning

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-binning

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/metawrap-binning:<tag>

(see metawrap-binning/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-blobology#

Versions:

1.3.0-3

Depends:

on blast 2.6.0.*
on bowtie2 2.3.5.*
on metawrap-mg >=1.3.0,<1.4.0a0
on perl-bioperl
on r-ggplot2 3.1.0.*
on r-recommended 3.5.1.*
on r-reshape2
on samtools 1.9.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-blobology

to add into an existing workspace instead, run:

pixi add metawrap-blobology

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 metawrap-blobology

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-blobology

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/metawrap-blobology:<tag>

(see metawrap-blobology/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-classify-bins#

Versions:

1.3.0-3

Depends:

on blast 2.6.0.*
on metawrap-mg >=1.3.0,<1.4.0a0
on taxator-tk 1.3.3e.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-classify-bins

to add into an existing workspace instead, run:

pixi add metawrap-classify-bins

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 metawrap-classify-bins

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-classify-bins

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/metawrap-classify-bins:<tag>

(see metawrap-classify-bins/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-kraken#

Versions:

1.3.0-3

Depends:

on jellyfish
on kraken 1.1.1.*
on kraken2 2.0.*
on krona 2.7.*
on metawrap-mg >=1.3.0,<1.4.0a0

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-kraken

to add into an existing workspace instead, run:

pixi add metawrap-kraken

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 metawrap-kraken

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-kraken

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/metawrap-kraken:<tag>

(see metawrap-kraken/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-mg#

Versions:

1.3.0-3, 1.3.0-1, 1.3.0-0

Depends:

on biopython 1.72.*
on python 2.7.15.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-mg

to add into an existing workspace instead, run:

pixi add metawrap-mg

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 metawrap-mg

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-mg

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/metawrap-mg:<tag>

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

Integrated deployment#

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package metawrap-quant-bins#

Versions:

1.3.0-3

Depends:

on matplotlib-base 2.2.5.*
on metawrap-mg >=1.3.0,<1.4.0a0
on pandas 0.24.2.*
on salmon 0.15.0.*
on seaborn 0.9.0.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-quant-bins

to add into an existing workspace instead, run:

pixi add metawrap-quant-bins

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 metawrap-quant-bins

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-quant-bins

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/metawrap-quant-bins:<tag>

(see metawrap-quant-bins/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-read-qc#

Versions:

1.3.0-3

Depends:

on bmtagger 3.101.*
on fastqc 0.11.8.*
on metawrap-mg >=1.3.0,<1.4.0a0
on trim-galore 0.5.0.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-read-qc

to add into an existing workspace instead, run:

pixi add metawrap-read-qc

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 metawrap-read-qc

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-read-qc

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/metawrap-read-qc:<tag>

(see metawrap-read-qc/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-reassemble-bins#

Versions:

1.3.0-3

Depends:

on bwa 0.7.17.*
on checkm-genome 1.0.12.*
on curl
on matplotlib-base 2.2.5.*
on metawrap-mg >=1.3.0,<1.4.0a0
on minimap2
on pplacer 1.1.alpha19.*
on spades 3.13.0.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-reassemble-bins

to add into an existing workspace instead, run:

pixi add metawrap-reassemble-bins

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 metawrap-reassemble-bins

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-reassemble-bins

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/metawrap-reassemble-bins:<tag>

(see metawrap-reassemble-bins/tags for valid values for <tag>).

Integrated deployment#

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package metawrap-refinement#

Versions:

1.3.0-3

Depends:

on checkm-genome 1.0.12.*
on curl
on jellyfish
on kraken 1.1.1.*
on krona 2.7.*
on matplotlib-base 2.2.5.*
on metawrap-mg >=1.3.0,<1.4.0a0
on pplacer 1.1.alpha19.*

Additional platforms:

Installation#

Pixi#

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

pixi global install metawrap-refinement

to add into an existing workspace instead, run:

pixi add metawrap-refinement

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 metawrap-refinement

Alternatively, to install into a new environment, run:

conda create -n envname metawrap-refinement

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/metawrap-refinement:<tag>

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

Integrated deployment#

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.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/metawrap-mg/README.html)