recipe ngseqbasic

Basic ChIP/DNaseI/ATAC analysis - from FASTQ to visualisation of tracks, in one command.

Homepage:

http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/instructionsBioconda.html

License:

GPL-3.0

Recipe:

/ngseqbasic/meta.yaml

package ngseqbasic

(downloads) docker_ngseqbasic

versions:

2.0.1-1,  2.0.1-0

depends bedtools:

==2.17.0

depends bowtie:

==1.0.0

depends bowtie2:

==2.3.0

depends flash:

==1.2.11

depends perl:

5.22.0.1

depends samtools:

==0.1.19

depends trim-galore:

==0.4.1

depends ucsc-bedclip:

==332

depends ucsc-bedgraphpack:

==332

depends ucsc-bedgraphtobigwig:

==332

depends ucsc-bedtobigbed:

==332

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 ngseqbasic

and update with::

   mamba update ngseqbasic

To create a new environment, run:

mamba create --name myenvname ngseqbasic

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/ngseqbasic:<tag>

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

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Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/ngseqbasic/README.html)