recipe gappa

Genesis Applications for Phylogenetic Placement Analysis

Homepage:

https://github.com/lczech/gappa

Documentation:

https://github.com/lczech/gappa/wiki

License:

GPL3 / GPL-3.0-only

Recipe:

/gappa/meta.yaml

Links:

doi: 10.1093/bioinformatics/btaa070, doi: 10.3389/fbinf.2022.871393, doi: 10.1093/bioinformatics/bty767, doi: 10.1371/journal.pone.0217050

gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data are typically produced by tools such as EPA-ng, RAxML-EPA or pplacer, and usually stored in jplace files.

package gappa

(downloads) docker_gappa

versions:
0.8.5-2,  0.8.5-1,  0.8.5-0,  0.8.4-1,  0.8.4-0,  0.8.0-3,  0.8.0-2,  0.8.0-1,  0.8.0-0, 

0.8.5-2,  0.8.5-1,  0.8.5-0,  0.8.4-1,  0.8.4-0,  0.8.0-3,  0.8.0-2,  0.8.0-1,  0.8.0-0,  0.7.1-1,  0.7.1-0,  0.7.0-1,  0.7.0-0,  0.6.1-0,  0.6.0-0,  0.5.1-0,  0.5.0-0,  0.4.0-0,  0.2.0-0,  0.1.0-0

depends _openmp_mutex:

>=4.5

depends libgcc:

>=12

depends libgomp:

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

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 gappa

and update with::

   mamba update gappa

To create a new environment, run:

mamba create --name myenvname gappa

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/gappa:<tag>

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

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