recipe damidseq_pipeline

An automated pipeline for processing DamID sequencing datasets

Homepage:

https://github.com/owenjm/damidseq_pipeline

License:

GPL-2.0

Recipe:

/damidseq_pipeline/meta.yaml

package damidseq_pipeline

versions:

1.5.3-0,  1.4-5,  1.4-4,  1.4-3,  1.4-2,  1.4-1,  1.4-0

depends bowtie2:

>=2.3.0

depends igvtools:

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends r-base:

depends samtools:

<1.3.0

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 damidseq_pipeline

and update with::

   mamba update damidseq_pipeline

To create a new environment, run:

mamba create --name myenvname damidseq_pipeline

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/damidseq_pipeline:<tag>

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

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Link to this page

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