recipe sapling

Inferring and Summarizing Tumor Phylogenies from Bulk DNA Data

Homepage:

https://github.com/elkebir-group/Sapling

Documentation:

https://github.com/elkebir-group/Sapling/blob/v1.0.0/README.md

License:

BSD / BSD-3-Clause

Recipe:

/sapling/meta.yaml

Sapling is a Python tool for inferring and summarizing tumor phylogenies from bulk DNA data. In addition to identifying full trees, Sapling also identifies "backbone trees" that summarize the space of plausible evolutionary histories. Sapling supports multiple solvers (fastPPM, CVXOPT, Gurobi) to estimate frequency matrices and infer high-likelihood trees.

package sapling

(downloads) docker_sapling

versions:

1.0.0-0

depends fastppm:

depends numpy:

depends pandas:

depends python:

>=3.6

depends tqdm:

requirements:

additional platforms:

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 sapling

and update with::

   mamba update sapling

To create a new environment, run:

mamba create --name myenvname sapling

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/sapling:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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