recipe haystack_bio

Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Homepage:

https://github.com/pinellolab/haystack_bio

License:

GPLv3

Recipe:

/haystack_bio/meta.yaml

package haystack_bio

versions:

0.5.5-1,  0.5.5-0,  0.5.4-1,  0.5.3-1,  0.5.3-0,  0.5.2-8,  0.5.2-7,  0.5.2-6,  0.5.2-5, 

0.5.5-1,  0.5.5-0,  0.5.4-1,  0.5.3-1,  0.5.3-0,  0.5.2-8,  0.5.2-7,  0.5.2-6,  0.5.2-5,  0.5.2-4,  0.5.2-3,  0.5.2-2,  0.5.2-1,  0.5.2-0,  v0.5.0-0

depends bedtools:

depends bx-python:

depends jinja2:

depends matplotlib:

depends meme:

4.11.2.*

depends numpy:

1.15.*

depends openjdk:

depends pandas:

depends python:

>=2.7,<3.0a0

depends sambamba:

depends scipy:

depends tqdm:

depends ucsc-bedgraphtobigwig:

depends ucsc-bigwigaverageoverbed:

depends weblogo:

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 haystack_bio

and update with::

   mamba update haystack_bio

To create a new environment, run:

mamba create --name myenvname haystack_bio

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/haystack_bio:<tag>

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

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Link to this page

Render an 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/haystack_bio/README.html)