recipe rad

Read-structure Agnostic Demultiplexer for long-read single-cell RNA-seq.

Homepage:

https://github.com/indianewok/rad

Documentation:

https://github.com/indianewok/rad/blob/v0.6.0/README.md

License:

MIT / MIT

Recipe:

/rad/meta.yaml

**rad** implements an alignment-based demultiplexer and whitelist/barcode-correction suite for Nanopore and PacBio single-cell long-read experiments. It bundles edlib and csv-parser in-tree, and depends only on Boost, zlib, and some flavor of openMP.

package rad

(downloads) docker_rad

versions:

0.6.0-0

depends _openmp_mutex:

>=4.5

depends boost-cpp:

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 rad

and update with::

   mamba update rad

To create a new environment, run:

mamba create --name myenvname rad

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/rad:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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