- recipe ampliconsuite
An end-to-end wrapper for focal amplification analysis from whole-genome sequencing using AmpliconArchitect and associated tools.
- Homepage:
- 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:
- package ampliconsuite¶
- Versions:
1.5.1-0,1.5.0-0,1.4.0-0,1.3.9-0,1.3.8-0,1.3.7-0,1.3.6-0,1.3.5-0,1.3.4-0,1.5.1-0,1.5.0-0,1.4.0-0,1.3.9-0,1.3.8-0,1.3.7-0,1.3.6-0,1.3.5-0,1.3.4-0,1.3.3-0,1.3.2-0,1.3.1-0,1.2.2-0,1.2.1-0,1.2.0-0,1.1.3-0,1.1.2-0,1.1.1-0,1.1.0-0,1.0.0-0,0.1555.2-1,0.1555.2-0- Depends:
on bedtools
on bwa
on cnvkit
>=0.9.10on flask
on future
on intervaltree
on matplotlib-base
on mscorefonts
on numpy
on pysam
on python
>=3on samtools
on scipy
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install ampliconsuite
to add into an existing workspace instead, run:
pixi add ampliconsuite
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install ampliconsuite
Alternatively, to install into a new environment, run:
conda create -n envname ampliconsuite
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/ampliconsuite:<tag>
(see ampliconsuite/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/ampliconsuite/README.html)
