recipe immuneml

immuneML is a software platform for machine learning analysis of immune receptor repertoires.

Homepage:

https://github.com/uio-bmi/immuneML

Documentation:

https://docs.immuneml.uio.no/

License:

AGPL / APGL-3.0-only

Recipe:

/immuneml/meta.yaml

package immuneml

versions:

2.2.6-1,  2.2.6-0,  2.2.5-1,  2.2.5-0,  2.2.4-1,  2.2.4-0,  2.2.3-0,  2.2.2-0,  2.2.0-0, 

2.2.6-1,  2.2.6-0,  2.2.5-1,  2.2.5-0,  2.2.4-1,  2.2.4-0,  2.2.3-0,  2.2.2-0,  2.2.0-0,  2.1.2-2,  2.1.2-1,  2.1.2-0,  2.1.1-1,  2.1.1-0,  2.1.0-0,  2.0.6-0,  2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  2.0.0-0,  1.2.5-0,  1.2.4-0,  1.2.0-0,  1.1.4-0,  1.1.3-1,  1.1.3-0

depends airr:

>=1

depends cython:

depends dill:

>=0.3

depends editdistance:

0.5.3

depends fishersapi:

depends gensim:

>=3.8,<4

depends h5py:

>=2.9.0

depends libgcc-ng:

>=12

depends logomaker:

>=0.8

depends matplotlib-base:

>=3.1

depends matplotlib-venn:

>=0.11

depends numpy:

>=1.18

depends pandas:

>=1

depends plotly:

>=4

depends pystache:

0.5.4

depends pytest:

>=4

depends python:

>=3.8,<3.9.0a0

depends python_abi:

3.8.* *_cp38

depends pytorch:

>=1.5.1

depends pyyaml:

>=5.3

depends regex:

depends requests:

>=2.21

depends scikit-learn:

>=0.23

depends scipy:

depends tensorboard:

>=1.14.0

depends tqdm:

>=0.24

depends tzlocal:

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 immuneml

and update with::

   mamba update immuneml

To create a new environment, run:

mamba create --name myenvname immuneml

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/immuneml:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/immuneml/README.html)