recipe gather

Assembly of heavy and light chain BCRs using De Bruijn graphs.

Homepage:

https://github.com/Neuroimmunology-UiO/gather

License:

MIT

Recipe:

/gather/meta.yaml

Gather is a Python-based toolkit for assembling heavy and light chain BCRs from sequence data using De Bruijn graphs. It includes modules for processing 10X and single-cell data.

package gather

versions:

0.1.0-0

depends argcomplete:

depends bcalm:

2.2.3.*

depends biopython:

depends joblib:

depends matplotlib-base:

depends networkx:

depends numpy:

>=1.19

depends pandas:

depends python:

>=3.9

depends rich:

depends tqdm:

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 gather

and update with::

   mamba update gather

To create a new environment, run:

mamba create --name myenvname gather

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/gather:<tag>

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

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