recipe gtotree

GToTree is a user-friendly workflow for phylogenomics.

Homepage:

https://github.com/AstrobioMike/GToTree/wiki/what-is-gtotree%3F

Documentation:

https://github.com/AstrobioMike/GToTree/wiki/

Developer docs:

https://github.com/AstrobioMike/GToTree/

License:

GPL / GPL3

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 -c defaults gtotree ```

package gtotree

versions:

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, 

1.8.5-0,  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 bc:

depends biopython:

depends coreutils:

9.1.*

depends curl:

depends dos2unix:

depends entrez-direct:

depends fasttree:

depends file:

depends gzip:

depends hmmer:

depends iqtree:

>=2.2.2

depends kofamscan:

1.3.0.*

depends muscle:

5.*

depends pandas:

depends parallel:

depends prodigal:

depends python:

depends sed:

depends taxonkit:

depends trimal:

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 gtotree

and update with::

   mamba update gtotree

To create a new environment, run:

mamba create --name myenvname gtotree

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/gtotree:<tag>

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

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