- recipe aacon
AACon: A Fast Amino Acid Conservation Calculation Service
- Homepage:
- Developer docs:
- License:
Apache-2.0
- Recipe:
- 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¶
- Versions:
1.1-0- Depends:
on openjdk
>=8
- 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 aacon
to add into an existing workspace instead, run:
pixi add aacon
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 aacon
Alternatively, to install into a new environment, run:
conda create -n envname aacon
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/aacon:<tag>
(see aacon/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.
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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Link to this page¶
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