recipe snakeatac_env

snakemake based ATACseq pipeline

Homepage:

https://github.com/sebastian-gregoricchio/snakeATAC

Documentation:

https://github.com/sebastian-gregoricchio/snakeATAC/wiki

License:

GPL-3.0-or-later

Recipe:

/snakeatac_env/meta.yaml

package snakeatac_env

versions:

0.1.1-0

depends bcftools:

depends bedtools:

depends bioconductor-copywriter:

depends bioconductor-shortread:

depends bioinfokit:

depends biopython:

depends bwa-mem2:

depends bzip2:

depends cutadapt:

depends deeptools:

>=3.5.2

depends docutils:

depends fastcluster:

depends fastqc:

depends gatk4:

depends logomaker:

depends macs3:

depends matplotlib-base:

depends multiqc:

>=1.23

depends numpydoc:

depends pandas:

depends pdfcombine:

depends pip:

depends py-bgzip:

depends py2bit:

depends pybedtools:

depends pybigwig:

depends pyfaidx:

depends pysam:

depends python:

depends r-colorspace:

depends r-data.table:

depends r-dplyr:

depends r-generics:

depends r-ggplot2:

depends r-ggtext:

depends r-plyr:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

depends r-snow:

depends r-stringr:

depends r-viridis:

depends samtools:

depends scipy:

depends seaborn:

depends snakemake:

>=7.24.0

depends snpsift:

depends subread:

depends tobias:

depends ucsc-bedgraphtobigwig:

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 snakeatac_env

and update with::

   mamba update snakeatac_env

To create a new environment, run:

mamba create --name myenvname snakeatac_env

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/snakeatac_env:<tag>

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

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