recipe roadies

Reference-free Orthology-free Alignment-free DIscordance aware Estimation of Species tree (ROADIES)

Homepage:

https://github.com/TurakhiaLab/ROADIES

Documentation:

https://turakhia.ucsd.edu/ROADIES/

License:

MIT / MIT

Recipe:

/roadies/meta.yaml

Links:

doi: 10.1101/2024.05.27.596098

ROADIES is an end-to-end pipeline designed for phylogenetic tree inference of the species directly from their raw genomic assemblies. ROADIES offers a fully automated, easy-to-use, scalable solution, eliminating any error-prone manual steps and providing unique flexibility in adjusting the tradeoff between accuracy and runtime.

package roadies

versions:

0.1.4-0

depends alive-progress:

depends biopython:

depends ete3:

depends fasttree:

>=2.1.11

depends libboost:

>=1.82.0,<1.83.0a0

depends libboost-devel:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends mashtree:

depends matplotlib-base:

depends numpy:

depends pasta:

>=1.9.0

depends pip:

depends python:

>=3.9,<3.10.0a0

depends python_abi:

3.9.* *_cp39

depends pyyaml:

depends raxml-ng:

depends seaborn:

depends snakemake:

depends treeswift:

>=1.1.28

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 roadies

and update with::

   mamba update roadies

To create a new environment, run:

mamba create --name myenvname roadies

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/roadies:<tag>

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

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