recipe ervmancer

Quantifies HERV short read RNA sequencing expression data

Homepage:

https://github.com/AuslanderLab/ervmancer

License:

MIT / MIT

Recipe:

/ervmancer/meta.yaml

ERVmancer quantifies Human Endogenous Retrovirus (HERV) short read RNA sequencing expression data by aligning short reads to a curated subset of HERVs and then resolves ambiguity in alignment using a pre-computed HERV phylogenetic tree.

package ervmancer

(downloads) docker_ervmancer

versions:

0.0.2-0,  0.0.1-0

depends bedtools:

>=2.29.2

depends bowtie2:

>=2.4.2

depends numpy:

depends pandas:

depends python:

>=3.8

depends regex:

depends samtools:

>=1.20

depends setuptools:

depends tqdm:

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 ervmancer

and update with::

   mamba update ervmancer

To create a new environment, run:

mamba create --name myenvname ervmancer

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/ervmancer:<tag>

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

Download stats

Link to this page

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

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