recipe freddie

Annotation-independent detection of splicing isoforms using RNA long-reads

Homepage:

https://github.com/vpc-ccg/freddie

License:

MIT

Recipe:

/freddie/meta.yaml

package freddie

versions:

0.4-0

depends desalt:

>=1.5.4

depends minimap2:

>=2.16

depends networkx:

>=2

depends numpy:

>=1.16

depends pysam:

>=0.15

depends python:

>=3.6

depends scikit-learn:

>=0.20

depends scipy:

>=1.2.1

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 freddie

and update with::

   mamba update freddie

To create a new environment, run:

mamba create --name myenvname freddie

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/freddie:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

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