recipe pangolin

Phylogenetic Assignment of Named Global Outbreak LINeages

Homepage:

https://github.com/cov-lineages/pangolin

License:

GPL-3.0-only

Recipe:

/pangolin/meta.yaml

Links:

usegalaxy-eu: pangolin

package pangolin

versions:

4.3.1-0,  4.3-2,  4.3-1,  4.3-0,  4.2-1,  4.2-0,  4.1.3-0,  4.1.2-2,  4.1.2-1, 

4.3.1-0,  4.3-2,  4.3-1,  4.3-0,  4.2-1,  4.2-0,  4.1.3-0,  4.1.2-2,  4.1.2-1,  4.1.2-0,  4.1.1-0,  4.1-0,  4.0.6-1,  4.0.6-0,  4.0.5-0,  4.0.4-0,  4.0.3-0,  4.0.2-1,  4.0.2-0,  4.0.1-0,  3.1.20-0,  3.1.19-0,  3.1.18-0,  3.1.17-1,  3.1.17-0,  3.1.16-2,  3.1.16-1,  3.1.16-0,  3.1.15-0,  3.1.14-1,  3.1.14-0,  3.1.11-2,  3.1.11-1,  3.1.11-0,  3.1.10-0,  3.1.9-0,  3.1.8-0,  3.1.7-0,  3.1.6-0,  3.1.5-0,  3.1.4-0,  3.1.3-0,  3.1.2-0,  3.0.5-0,  3.0.3-0,  2.4.2-1,  2.4.2-0,  2.4-0,  2.3.8-0,  2.3.6-0,  2.3.5-0,  2.3.4-0,  2.3.2-0,  2.3.0-1,  2.3.0-0,  2.2.2-0,  2.2.1-0,  2.1.11-0,  2.1.10-1,  2.1.10-0,  2.1.7-0,  1.1.14-0,  1.1.13-0,  1.1.11-0,  1.1.5-0,  1.1-0

depends biopython:

>=1.74

depends conda:

depends constellations:

>=0.0.15

depends git:

depends git-lfs:

depends gofasta:

depends joblib:

>=0.11

depends minimap2:

>=2.16

depends pandas:

>=1.0.1

depends pangolin-data:

>=1.2.133.2

depends pulp:

>=2

depends python:

>=3.7

depends scikit-learn:

>=0.23.1,<1.3.0

depends scorpio:

>=0.3.12

depends snakemake-minimal:

>=5.13,!=7.30.1,<8

depends ucsc-fatovcf:

>=426

depends usher:

>=0.6.2

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 pangolin

and update with::

   mamba update pangolin

To create a new environment, run:

mamba create --name myenvname pangolin

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/pangolin:<tag>

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

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