recipe liquorice

A tool for bias correction and quantification of changes in coverage around regions of interest in cfDNA WGS datasets

Homepage:

https://github.com/epigen/LIQUORICE

License:

GPL / GPL-3.0

Recipe:

/liquorice/meta.yaml

See https://liquorice.readthedocs.io for more information.

package liquorice

versions:

0.5.6-0,  0.5.5-1,  0.5.5-0,  0.5.4-0,  0.5.3-0

depends biopython:

1.79

depends deeptools:

3.5.1

depends joblib:

1.0.1

depends lmfit:

1.0.2

depends matplotlib-base:

3.1.1

depends modin:

0.8.2

depends numpy:

1.21.2

depends pandas:

1.1.4

depends parallel:

depends pybedtools:

0.8.2

depends pybigwig:

0.3.18

depends pysam:

0.16.0.1

depends python:

>=3.7.9

depends scikit-learn:

0.24.2

depends scipy:

1.7.1

depends seaborn:

0.11.2

depends swifter:

1.0.9

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 liquorice

and update with::

   mamba update liquorice

To create a new environment, run:

mamba create --name myenvname liquorice

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/liquorice:<tag>

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

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