recipe longcallr_nn

longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model.

Homepage:

https://github.com/huangnengCSU/longcallR-nn

License:

MIT / MIT

Recipe:

/longcallr_nn/meta.yaml

package longcallr_nn

versions:

0.0.1-1,  0.0.1-0

depends numpy:

>=1.21.0

depends pysam:

>=0.16

depends python:

>=3.9,<3.11

depends pytorch:

>=1.13

depends pyyaml:

>=5.3

depends requests:

depends tensorboardx:

>=2.2

depends torchmetrics:

>=0.9

depends torchvision:

>=0.14

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 longcallr_nn

and update with::

   mamba update longcallr_nn

To create a new environment, run:

mamba create --name myenvname longcallr_nn

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/longcallr_nn:<tag>

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

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Link to this page

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