Package Recipe 'roadies'

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:

0.1.10-0, 0.1.8-0, 0.1.4-0

Depends:

on alive-progress
on aster >=1.19
on biopython
on boost-cpp
on ete3
on fasttree >=2.1.11
on lastz >=1.04.52
on libgcc >=13
on libstdcxx >=13
on libzlib >=1.2.13,<2.0a0
on mash >=2
on mashtree 1.4.6
on matplotlib-base
on numpy
on pasta >=1.9.0
on perl >=5.22
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-bioperl >=1.7.2
on perl-module-build 0.4234.*
on python >=3.9,<3.10.0a0
on python_abi 3.9.* *_cp39
on pyyaml
on quicktree
on raxml-ng
on seaborn-base
on snakemake-minimal
on treeswift >=1.1.28

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 roadies

to add into an existing workspace instead, run:

pixi add roadies

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 roadies

Alternatively, to install into a new environment, run:

conda create -n envname roadies

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/roadies:<tag>

(see roadies/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:

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