recipe aacon

AACon: A Fast Amino Acid Conservation Calculation Service

Homepage:

https://www.compbio.dundee.ac.uk/aacon/

Developer docs:

https://github.com/bartongroup/aacon

License:

Apache-2.0

Recipe:

/aacon/meta.yaml

Links:

biotools: aacon

AACon is a set of tools implementing 17 different conservation scores reviewed by Valdar as well as the more complex SMERFS algorithm for predicting protein functional sites. AACon has been written with efficiency in mind and takes less than a second to calculate conservation by all 18 methods for an alignment of 500 sequences 350 residues long on a single CPU. AACon exploits parallelism for the more demanding methods and to allow multiple methods to run simultaneously. The parallel code gives close to linear speedup with the number of processors, thus making it suitable for server applications or other demanding environments.

package aacon

(downloads) docker_aacon

versions:

1.1-0

depends openjdk:

>=8

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 aacon

and update with::

   mamba update aacon

To create a new environment, run:

mamba create --name myenvname aacon

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/aacon:<tag>

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

Notes

AACon is a Java program that comes with a custom wrapper shell script. The shell wrapper is called "aacon" and is present on $PATH by default. The Java program is executed with java specified by the $JAVA_HOME variable. Otherwise, a "java" program from the current environment is used.

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