recipe uropa

UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding.

Homepage:

https://github.com/loosolab/UROPA

Documentation:

http://uropa-manual.readthedocs.io

License:

MIT / MIT

Recipe:

/uropa/meta.yaml

package uropa

versions:

4.0.3-0,  4.0.2-0,  4.0.1-0,  4.0.0-0,  3.5.3-0,  3.5.2-0,  3.5.0-0,  3.4.0-0,  3.3.4-0, 

4.0.3-0,  4.0.2-0,  4.0.1-0,  4.0.0-0,  3.5.3-0,  3.5.2-0,  3.5.0-0,  3.4.0-0,  3.3.4-0,  3.3.3-0,  3.3.2-0,  3.3.0-0,  3.2.0-0,  3.1.0-0,  3.0.0-0,  2.0.3-0,  2.0.2a0-2,  2.0.2a0-0,  2.0.0a0-0,  1.2.1-0

depends bioconductor-graph:

depends bioconductor-rbgl:

depends numpy:

depends psutil:

depends pysam:

>=0.15.3

depends python:

>=3.6

depends r-base:

depends r-getopt:

depends r-ggplot2:

depends r-gplots:

depends r-gridextra:

depends r-jsonlite:

depends r-tidyr:

depends r-upsetr:

depends r-venndiagram:

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 uropa

and update with::

   mamba update uropa

To create a new environment, run:

mamba create --name myenvname uropa

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/uropa:<tag>

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

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