recipe slncky

slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution. slncky was developed as a collaboration between the Garber Lab at UMass Medical and the Regev Lab at the Broad Institute.

Homepage:

https://github.com/slncky/slncky

License:

MIT / MIT

Recipe:

/slncky/meta.yaml

package slncky

(downloads) docker_slncky

versions:

1.0.4-2,  1.0.4-1,  1.0.4-0,  1.0.3-0

depends bedtools:

>=2.17.0,<=2.24.0

depends lastz:

depends numpy:

depends python:

<3

depends ucsc-liftover:

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 slncky

and update with::

   mamba update slncky

To create a new environment, run:

mamba create --name myenvname slncky

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/slncky:<tag>

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

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Link to this page

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