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

Links:

biotools: immuneml, doi: 10.1038/s42256-021-00413-z

package immuneml

versions:

3.0.14-0,  3.0.12-0,  3.0.11-0,  3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-1,  3.0.6-0,  3.0.5-0, 

3.0.14-0,  3.0.12-0,  3.0.11-0,  3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-1,  3.0.6-0,  3.0.5-0,  3.0.4-0,  3.0.3-0,  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,<1.4

depends bionumpy:

1.0.12

depends dill:

>=0.3

depends editdistance:

depends gensim:

>=4

depends keras:

>=2.12.0

depends logomaker:

>=0.8

depends matplotlib-base:

>=3.1

depends matplotlib-venn:

>=0.11

depends npstructures:

depends numpy:

<=1.26.4

depends olga:

>=1.2.4

depends pandas:

>=2.1.0

depends plotly:

>=4

depends psutil:

depends pystache:

depends pytest:

>=4

depends python:

>=3.7,<3.12

depends python-kaleido:

depends pytorch:

>=2.* cpu_*

depends pyyaml:

>=5.3

depends regex:

depends scikit-learn:

>=0.23

depends scipy:

<1.13

depends tensorflow:

>=2.12.0

depends tzlocal:

depends umap-learn:

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 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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