recipe irescue

A tool to quantify transposable elements expression in scRNA-seq.

Homepage:

https://github.com/bodegalab/irescue

Documentation:

https://pypi.org/project/IRescue

License:

MIT / MIT

Recipe:

/irescue/meta.yaml

Links:

doi: 10.1101/2022.09.16.508229

package irescue

versions:

1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.3-1,  1.0.3-0,  1.0.2-0,  1.0.1-0

depends bedtools:

>=2.30.0

depends coreutils:

>=9.3

depends gawk:

>=5.0.1

depends gzip:

>=1.12

depends networkx:

>=3.1

depends numpy:

>=1.20.2

depends pysam:

>=0.16.0.1

depends python:

>=3.8

depends requests:

>=2.27.1

depends samtools:

>=1.12

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 irescue

and update with::

   mamba update irescue

To create a new environment, run:

mamba create --name myenvname irescue

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/irescue:<tag>

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

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