recipe get_pangenes

A versatile software package for calling pangenes from whole genome alignments

Homepage:

https://github.com/Ensembl/plant-scripts/tree/master/pangenes

License:

APACHE / Apache-2.0

Recipe:

/get_pangenes/meta.yaml

Links:

doi: https://doi.org/10.1186/s13059-023-03071-z

get_pangenes.pl computes whole genome alignments (WGA) to define clusters of collinear, orthologous genes/features annotated in GFF files, defining pangenes across a pangenome. currently the bioconda version supports nly minimap2.

package get_pangenes

(downloads) docker_get_pangenes

versions:

20250123-0

depends bedtools:

depends bzip2:

depends coreutils:

depends get_homologues:

depends gffread:

0.12.7.*

depends gmap:

depends grep:

depends gsalign:

depends gzip:

depends minimap2:

2.24.*

depends perl:

depends perl-db_file:

depends samtools:

depends wget:

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 get_pangenes

and update with::

   mamba update get_pangenes

To create a new environment, run:

mamba create --name myenvname get_pangenes

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/get_pangenes:<tag>

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

Notes

This package installs the GET_PANGENES code. It is recommended to run it in a computer cluster with LSF or slurm, particularly for large genomes. To configure it for HPC (get_pangenes.pl -m) please check the documentation and edit your own HPC.conf file , which should be placed in the same location as the main script get_pangenes.pl . Documentation can be found at

https://github.com/Ensembl/plant-scripts/tree/master/pangenes

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