recipe ampliconsuite

An end-to-end wrapper for focal amplification analysis from whole-genome sequencing using AmpliconArchitect and associated tools.

Homepage:

https://github.com/AmpliconSuite

License:

BSD 2-Clause License (AmpliconSuite-pipeline and AmpliconClassifier) & University of California Software License (AmpliconArchitect). Please see https://github.com/AmpliconSuite/AmpliconSuite-pipeline for more details on licenses.

Recipe:

/ampliconsuite/meta.yaml

package ampliconsuite

versions:

1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.3-0,  1.1.2-0, 

1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.2.2-0,  1.2.1-0,  1.2.0-0,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.0-0,  0.1555.2-1,  0.1555.2-0

depends bedtools:

depends bwa:

depends cnvkit:

>=0.9.10

depends flask:

depends future:

depends intervaltree:

depends matplotlib-base:

depends mscorefonts:

depends numpy:

depends pysam:

depends python:

>=3

depends samtools:

depends scipy:

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 ampliconsuite

and update with::

   mamba update ampliconsuite

To create a new environment, run:

mamba create --name myenvname ampliconsuite

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/ampliconsuite:<tag>

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

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