recipe cats-rf

Reference-free transcriptome assembly quality assessment tool.

Homepage:

https://github.com/bodulic/CATS-rf

Documentation:

https://github.com/bodulic/CATS-rf/blob/main/README.md

License:

MIT

Recipe:

/cats-rf/meta.yaml

CATS-rf evaluates transcriptome assemblies using RNA-seq reads without requiring a reference genome.

package cats-rf

versions:

1.0.0-0

depends bash:

depends bedtools:

depends bowtie2:

depends coreutils:

depends gawk:

depends kallisto:

depends pandoc:

depends parallel:

>=20220922

depends pysamstats:

depends python:

>=3.6

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggdist:

depends r-ggplot2:

depends r-rmarkdown:

depends samtools:

depends sed:

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 cats-rf

and update with::

   mamba update cats-rf

To create a new environment, run:

mamba create --name myenvname cats-rf

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/cats-rf:<tag>

(see `cats-rf/tags`_ for valid values for ``<tag>``)

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Link to this page

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