- 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:
- Links:
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¶
- Versions:
20250904-0,20250123-0,1.3-0- Depends:
on bedtools
on bzip2
on coreutils
on get_homologues
on gffread
0.12.7.*on gmap
on grep
on gsalign
on gzip
on minimap2
2.24.*on perl
on perl-db_file
on samtools
on wget
- 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 get_pangenes
to add into an existing workspace instead, run:
pixi add get_pangenes
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 get_pangenes
Alternatively, to install into a new environment, run:
conda create -n envname get_pangenes
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/get_pangenes:<tag>
(see get_pangenes/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.
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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Link to this page¶
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