recipe midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

Homepage:

https://github.com/snayfach/MIDAS

License:

GPL / GPL-3.0

Recipe:

/midas/meta.yaml

package midas

versions:

1.3.2-7,  1.3.2-6,  1.3.2-5,  1.3.2-4,  1.3.2-3,  1.3.2-2,  1.3.2-0,  1.3.1-0,  1.3.0-0, 

1.3.2-7,  1.3.2-6,  1.3.2-5,  1.3.2-4,  1.3.2-3,  1.3.2-2,  1.3.2-0,  1.3.1-0,  1.3.0-0,  1.2.2-1,  1.2.2-0

depends biopython:

>=1.6.2

depends bowtie2:

2.3.2.*

depends hs-blastn:

depends numpy:

>=1.7.0

depends pandas:

>=0.17.1

depends pysam:

>=0.8.1

depends python:

>=2.7

depends samtools:

1.4.0.*

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 midas

and update with::

   mamba update midas

To create a new environment, run:

mamba create --name myenvname midas

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/midas:<tag>

(see `midas/tags`_ for valid values for ``<tag>``)

Notes

MIDAS requires reference database that needs to be additionally downloaded and set, https://github.com/snayfach/MIDAS/blob/master/docs/ref_db.md.

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