recipe alloshp

From mapped reads to Single Homeologous Polymorphisms (SHPs): pipeline for phylogenetic studies of allopolyploids

Homepage:

https://github.com/eead-csic-compbio/AlloSHP

License:

APACHE / Apache-2.0

Recipe:

/alloshp/meta.yaml

Links:

doi: 10.1101/2025.07.17.665301

This 3-step protocol computes Whole Genome Alignments (WGA) to discover Single Homeologous Polymorphisms (SHPs) out of reads mapped to concatenated genome sequeces. It requires FASTA and VCF input files and produces multiple sequence alignments of subgenomes that make up allopolyploids.

package alloshp

versions:

2025.09.08-0,  2025.09.08d-0

depends bzip2:

depends coreutils:

depends gnuplot:

depends grep:

depends gsalign:

depends gzip:

depends perl:

depends perl-db_file:

depends red:

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 alloshp

and update with::

   mamba update alloshp

To create a new environment, run:

mamba create --name myenvname alloshp

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/alloshp:<tag>

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

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