recipe gembs

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

Homepage:

https://github.com/heathsc/gemBS

License:

GPL-3.0

Recipe:

/gembs/meta.yaml

Links:

doi: 10.1101/201988

package gembs

versions:

3.5.5_IHEC-8,  3.5.5_IHEC-7,  3.5.5_IHEC-6,  3.5.5_IHEC-5,  3.5.5_IHEC-4,  3.5.5_IHEC-3,  3.5.5_IHEC-2,  3.5.5_IHEC-1,  3.5.5_IHEC-0, 

3.5.5_IHEC-8,  3.5.5_IHEC-7,  3.5.5_IHEC-6,  3.5.5_IHEC-5,  3.5.5_IHEC-4,  3.5.5_IHEC-3,  3.5.5_IHEC-2,  3.5.5_IHEC-1,  3.5.5_IHEC-0,  3.5.1_IHEC-0,  3.5.0-1,  3.5.0-0,  3.2.0-5,  3.2.0-4,  3.2.0-3,  3.2.0-2,  3.2.0-1,  3.2.0-0

depends bcftools:

depends bs_call:

depends bzip2:

>=1.0.8,<2.0a0

depends gem3-mapper:

depends htslib:

>=1.20,<1.22.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends matplotlib-base:

depends multiprocess:

depends openssl:

>=3.3.1,<4.0a0

depends pigz:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends samtools:

depends setuptools:

depends ucsc-bedtobigbed:

depends ucsc-wigtobigwig:

depends zlib:

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 gembs

and update with::

   mamba update gembs

To create a new environment, run:

mamba create --name myenvname gembs

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/gembs:<tag>

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

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