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:
0.9.0-0,  0.8.5-3,  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, 

0.9.0-0,  0.8.5-3,  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:

  • on _openmp_mutex >=4.5

  • on libgcc >=13

  • on libgomp

  • on libstdcxx >=13

  • on libzlib >=1.3.1,<2.0a0

Additional platforms:
linux-aarch64,  osx-arm64

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 gappa

to add into an existing workspace instead, run:

pixi add gappa

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 gappa

Alternatively, to install into a new environment, run:

conda create -n envname gappa

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/gappa:<tag>

(see gappa/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.

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