recipe stopfree

Rust implementation of the stopFree coding potential tool

Homepage:

https://github.com/afg1/stopfree

Documentation:

https://pypi.org/project/stopfree/

License:

Apache-2.0

Recipe:

/stopfree/meta.yaml

A fast Rust implementation (with Python bindings via PyO3) of the stopFree coding potential tool. It measures the longest stop codon free length of sequence in each of the 6 possible reading frames, calculates per-sequence GC content, and computes the probability of observing a stop-free run of the given length under an iid model corrected for GC content.

package stopfree

(downloads) docker_stopfree

versions:

0.2.4-0

depends libgcc:

>=14

depends python:

>=3.14,<3.15.0a0

depends python_abi:

3.14.* *_cp314

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 stopfree

and update with::

   mamba update stopfree

To create a new environment, run:

mamba create --name myenvname stopfree

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/stopfree:<tag>

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

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Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/stopfree/README.html)