recipe rnabloom

Java tool for RNA-seq assembly

Homepage:

https://github.com/bcgsc/RNA-Bloom

Documentation:

https://github.com/bcgsc/RNA-Bloom/blob/master/README.md

License:

GPL-3.0

Recipe:

/rnabloom/meta.yaml

Links:

doi: 10.1101/gr.260174.119, doi: 10.1038/s41467-023-38553-y

RNA-Bloom is a reference-free and reference-guided transcriptome assembly tool for short and long RNA-seq reads.

package rnabloom

(downloads) docker_rnabloom

versions:
2.0.1-1,  2.0.1-0,  2.0.0-0,  1.4.3-0,  1.3.1-2,  1.3.1-1,  1.3.1-0,  1.3.0-0,  1.2.3-0, 

2.0.1-1,  2.0.1-0,  2.0.0-0,  1.4.3-0,  1.3.1-2,  1.3.1-1,  1.3.1-0,  1.3.0-0,  1.2.3-0,  1.2.2-0

depends minimap2:

depends ntcard:

>=1.2.1

depends openjdk:

>=11

depends racon:

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 rnabloom

and update with::

   mamba update rnabloom

To create a new environment, run:

mamba create --name myenvname rnabloom

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/rnabloom:<tag>

(see `rnabloom/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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