recipe pggb

This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model).

Homepage:

https://github.com/pangenome/pggb

License:

MIT

Recipe:

/pggb/meta.yaml

package pggb

versions:

0.6.0-0,  0.5.4-0,  0.5.3-2,  0.5.3-1,  0.5.3-0,  0.5.2-0,  0.5.1-1,  0.5.1-0,  0.5.0-0, 

0.6.0-0,  0.5.4-0,  0.5.3-2,  0.5.3-1,  0.5.3-0,  0.5.2-0,  0.5.1-1,  0.5.1-0,  0.5.0-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.1-1,  0.3.1-0,  0.3.0-1,  0.3.0-0,  0.2.0-0

depends bc:

depends bcftools:

depends gfaffix:

0.1.5b

depends gsl:

2.7.0.*

depends multiqc:

1.19

depends odgi:

0.8.6

depends pigz:

depends python-igraph:

0.10.4

depends seqwish:

0.7.10

depends smoothxg:

0.7.4

depends tabix:

depends time:

depends vg:

1.40.0.*

depends wfmash:

0.13.0

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 pggb

and update with::

   mamba update pggb

To create a new environment, run:

mamba create --name myenvname pggb

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/pggb:<tag>

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

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