Package Recipe 'roadies' — Bioconda documentation

recipe roadies

Reference-free, orthology-free, discordance-aware species tree estimation from raw genome assemblies.

Homepage:: 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. ROADIES_XP extends this with GPU-accelerated alignment/tree-building and a placement mode for growing or updating an existing species tree with new genomes.

package roadies#

Versions:

0.2.0-0, 0.1.10-0, 0.1.8-0, 0.1.4-0

Depends:

on __osx >=10.13
on alive-progress
on aster >=1.19
on biopython
on boost-cpp
on epa-ng
on ete3
on fasttree >=2.1.11
on gappa
on lastz >=1.04.52
on libblas >=3.9.0,<4.0a0
on libcxx >=19
on liblapack >=3.9.0,<4.0a0
on libzlib >=1.3.2,<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 >=3.11,<3.12.0a0
on python_abi 3.11.* *_cp311
on pyyaml
on quicktree
on raxml-ng
on seaborn-base
on snakemake-minimal
on tbb >=2022.3.0
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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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)