recipe pantax

Strain-level taxonomic classification of metagenomic data using pangenome graphs

Homepage:

https://github.com/LuoGroup2023/PanTax

License:

GPL3 / GPL-3.0-or-later

Recipe:

/pantax/meta.yaml

package pantax

versions:

1.0.2-0

depends bcftools:

1.19.*

depends graphaligner:

1.0.17.*

depends h5py:

3.10.0.*

depends htslib:

1.19.1.*

depends networkx:

3.2.1.*

depends numpy:

1.26.3.*

depends pandas:

2.2.0.*

depends pggb:

0.6.0.*

depends pyarrow:

14.0.2.*

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

1.19.2.*

depends tqdm:

depends vg:

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 pantax

and update with::

   mamba update pantax

To create a new environment, run:

mamba create --name myenvname pantax

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/pantax:<tag>

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

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