recipe chiron

A deep neural network basecaller for nanopore sequencing.

Homepage:

https://github.com/haotianteng/chiron

License:

OTHER / Mozilla Public License 2.0 (MPL 2.0)

Recipe:

/chiron/meta.yaml

Links:

doi: 10.1093/gigascience/giy037, biotools: Chiron

package chiron

versions:

0.6.1.1-0,  0.6.1-0,  0.4.2.1-1,  0.4.2.1-0

depends h5py:

>=2.7.0

depends mappy:

>=2.10.0

depends numpy:

>=1.13.3

depends python:

2.7.*

depends statsmodels:

>=0.8.0

depends tensorflow:

>=1.3.0

depends tqdm:

>=4.23.0

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 chiron

and update with::

   mamba update chiron

To create a new environment, run:

mamba create --name myenvname chiron

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/chiron:<tag>

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

Notes

conda-forge::tensorflow requires GLIBC >=2.16. It should be present on most, but not all systems. See https://github.com/conda-forge/tensorflow-feedstock/issues/67

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