recipe neoloop

Predict neo-loops induced by structural variations

Homepage:

https://github.com/XiaoTaoWang/NeoLoopFinder

License:

OTHER / https://github.com/XiaoTaoWang/NeoLoopFinder/blob/master/LICENSE

Recipe:

/neoloop/meta.yaml

package neoloop

versions:

0.4.3.post2-0

depends cooler:

depends h5py:

depends intervaltree:

depends joblib:

1.1.0.*

depends matplotlib-base:

depends networkx:

depends numpy:

depends pandas:

depends pomegranate:

0.14.8.*

depends pybigwig:

depends pyensembl:

depends python:

>=3.6

depends r-base:

depends r-mgcv:

depends rpy2:

depends scikit-learn:

1.1.2.*

depends scipy:

depends tadlib:

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 neoloop

and update with::

   mamba update neoloop

To create a new environment, run:

mamba create --name myenvname neoloop

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/neoloop:<tag>

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

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