Package Recipe 'gtotree'

recipe gtotree

GToTree is a user-friendly workflow for phylogenomics.

Homepage:: https://github.com/AstrobioMike/GToTree
Documentation:: https://github.com/AstrobioMike/GToTree/wiki
License:: GPL3 / GPL-3.0-or-later
Recipe:: /gtotree/meta.yaml

# GToTree - a user-friendly workflow for phylogenomics

GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees. The open-access Bioinformatics Journal publication is available here (https://doi.org/10.1093/bioinformatics/btz188), and documentation and examples can be found at the wiki here (https://github.com/AstrobioMike/GToTree/wiki).

Installation should be performed as:

``` conda create -n gtotree -c astrobiomike -c conda-forge -c bioconda gtotree ```

package gtotree¶

Versions:

1.8.16-2, 1.8.16-1, 1.8.16-0, 1.8.15-0, 1.8.14-0, 1.8.13-0, 1.8.12-0, 1.8.11-0, 1.8.10-0,

1.8.16-2, 1.8.16-1, 1.8.16-0, 1.8.15-0, 1.8.14-0, 1.8.13-0, 1.8.12-0, 1.8.11-0, 1.8.10-0, 1.8.9-0, 1.8.8-1, 1.8.8-0, 1.8.7-0, 1.8.6-0, 1.8.5-0, 1.8.4-0, 1.8.3-0, 1.8.2-0, 1.8.1-0, 1.7.10-0, 1.7.08-0, 1.7.07-0, 1.7.06-0, 1.7.05-1

Depends:

on bc
on biopython
on coreutils 9.1.*
on curl
on dos2unix
on entrez-direct
on fasttree 2.1.11.*
on file
on gzip
on hmmer
on iqtree >=2.2.2
on kofamscan 1.3.0.*
on muscle 5.1.*
on pandas
on parallel
on prodigal
on pyarrow
on python 3.12.7.*
on sed
on tar
on taxonkit
on trimal
on veryfasttree

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 gtotree

to add into an existing workspace instead, run:

pixi add gtotree

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 gtotree

Alternatively, to install into a new environment, run:

conda create -n envname gtotree

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/gtotree:<tag>

(see gtotree/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/gtotree/README.html)