recipe ctseq

ctSeq is a pipeline to analyze methylation patch PCR data

Homepage:

https://github.com/ryanhmiller/ctseq

License:

MIT / MIT

Recipe:

/ctseq/meta.yaml

package ctseq

versions:

0.0.2-0

depends bismark:

depends cutadapt:

depends ncurses:

6.1 he6710b0_1

depends numpy:

depends openssl:

1.0.2p h14c3975_1002

depends python:

>=3.7

depends r-base:

3.5.1.*

depends r-ggplot2:

depends r-pheatmap:

depends r-reshape:

depends samtools:

1.9.*

depends simplesam:

0.1.3.1.*

depends umi_tools:

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 ctseq

and update with::

   mamba update ctseq

To create a new environment, run:

mamba create --name myenvname ctseq

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/ctseq:<tag>

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

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