recipe flair

Correction, isoform definition, and alternative splicing analysis of noisy reads (ONT and PacBio).

Homepage:

https://github.com/BrooksLabUCSC/flair

License:

BSD-3

Recipe:

/flair/meta.yaml

Links:

doi: 10.1101/410183

package flair

versions:

2.0.0-1,  2.0.0-0,  1.7.0-1,  1.7.0-0,  1.6.4-0,  1.6.3-0,  1.5-4,  1.5-3,  1.4-0

depends bedtools:

depends bioconductor-apeglm:

depends bioconductor-deseq2:

depends bioconductor-drimseq:

depends bioconductor-stager:

depends mappy:

2.24.*

depends matplotlib-base:

depends minimap2:

2.24.*

depends ncls:

depends pandas:

depends pybedtools:

depends pysam:

depends python:

>=3.6

depends r-ggplot2:

depends r-lazyeval:

depends r-qqman:

depends rpy2:

depends samtools:

depends scipy:

depends seaborn-base:

depends tqdm:

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 flair

and update with::

   mamba update flair

To create a new environment, run:

mamba create --name myenvname flair

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/flair:<tag>

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

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