recipe ccsmeth

Detecting DNA methylation from PacBio CCS read

Homepage:

https://github.com/PengNi/ccsmeth

License:

BSD / BSD-3-Clause-Clear

Recipe:

/ccsmeth/meta.yaml

package ccsmeth

versions:

0.5.0-0,  0.4.1-0,  0.4.0-0,  0.3.4-0,  0.3.2-0,  0.3.1-0

depends bedtools:

2.30.0.*

depends numpy:

>=1.20.0

depends pbccs:

>=6.4.0

depends pbmm2:

>=1.9.0

depends pybedtools:

>=0.8.1

depends pysam:

>=0.19.0

depends pytabix:

>=0.1

depends python:

>=3.8

depends pytorch:

>=1.2.0,<=2.1.0

depends samtools:

>=1.12

depends scikit-learn:

>=1.0.2

depends setuptools:

depends statsmodels:

>=0.13.2

depends tqdm:

>=4.64.0

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 ccsmeth

and update with::

   mamba update ccsmeth

To create a new environment, run:

mamba create --name myenvname ccsmeth

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/ccsmeth:<tag>

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

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