recipe grid

Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at ultra-low sequencing coverage (> 0.2x).

Homepage:

https://github.com/ohlab/GRiD

License:

MIT

Recipe:

/grid/meta.yaml

package grid

versions:

1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.2-0,  1.1-4,  1.1-3,  1.1-2,  1.1-1, 

1.3-3,  1.3-2,  1.3-1,  1.3-0,  1.2-0,  1.1-4,  1.1-3,  1.1-2,  1.1-1,  1.1-0,  1.0.6-0

depends bamtools:

depends bedtools:

depends blast:

depends bowtie2:

depends mosdepth:

depends parallel:

depends pathoscope:

depends r-dplyr:

depends r-getopt:

depends r-ggplot2:

depends r-gplots:

depends r-gsubfn:

depends readline:

>=6.2

depends samtools:

depends seqtk:

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 grid

and update with::

   mamba update grid

To create a new environment, run:

mamba create --name myenvname grid

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/grid:<tag>

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

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