recipe halfdeep

Automated detection of intervals covered at half depth by sequenced reads.

Homepage:

https://github.com/richard-burhans/HalfDeep

License:

BSD-3-Clause

Recipe:

/halfdeep/meta.yaml

package halfdeep

versions:

0.1.0-0

depends bash:

depends coreutils:

depends gawk:

depends genodsp:

depends grep:

depends gzip:

depends minimap2:

depends python:

>=3.9

depends r-base:

>=4.3.*

depends samtools:

depends sed:

requirements:

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 halfdeep

and update with::

   mamba update halfdeep

To create a new environment, run:

mamba create --name myenvname halfdeep

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/halfdeep:<tag>

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

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