- recipe hatchet
A package to infer allele and clone-specific copy-number aberrations (CNAs).
- Homepage:
- Documentation:
- License:
BSD / BSD-3-Clause
- Recipe:
HATCHet is an algorithm to infer allele and clone-specific copy-number aberrations (CNAs), clone proportions, and whole-genome duplications (WGD) for several tumor clones jointly from multiple bulk-tumor samples of the same patient or from a single bulk-tumor sample.
- package hatchet¶
- Versions:
2.2.0-0,2.1.2-0,2.1.1-1,2.1.1-0,2.1.0-2,2.1.0-1,2.1.0-0,2.0.1-1,2.0.1-0,2.2.0-0,2.1.2-0,2.1.1-1,2.1.1-0,2.1.0-2,2.1.0-1,2.1.0-0,2.0.1-1,2.0.1-0,1.1.1-1,1.1.1-0,1.1.0-0,1.0.3-0,1.0.2-0,1.0.1-0,1.0.0-0,0.4.14-0,0.4.12-1,0.4.12-0,0.4.11-0,0.4.10-0,0.4.9-0,0.4.7-0,0.4.6-0,0.4.5-0,0.4.4-0,0.4.3-0,0.4.2-0,0.4.1-0,0.3.3-0,0.3.2-0,0.3.1-0,0.3.0-0,0.2.11-0,0.2.10-0,0.2.9-3,0.2.9-1,0.2.9-0- Depends:
on bcftools
on biopython
on hmmlearn
on kneed
on libgcc
>=14on libstdcxx
>=14on matplotlib-base
on mosdepth
on numpy
>=1.13,<2on pandas
on picard-slim
on psutil
on pybedtools
on pyomo
on pysam
on python
>=3.10,<3.11.0a0on python_abi
3.10.* *_cp310on requests
on samtools
on scikit-learn
on scipy
on seaborn-base
on statsmodels
on tabix
- 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 hatchet
to add into an existing workspace instead, run:
pixi add hatchet
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 hatchet
Alternatively, to install into a new environment, run:
conda create -n envname hatchet
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/hatchet:<tag>
(see hatchet/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/hatchet/README.html)
