jnpsolutions/slacken repository overview

Slacken is a genomic sequence classification tool that improves on the Kraken 2 method. For more details see the GitHub repo (https://github.com/JNP-Solutions/Slacken⁠).

This docker image is intended to simplify running Slacken in standalone (single machine) mode. It builds on the official Apache Spark image, bundling it together with Slacken.

Slacken may be run from this image in the following way, for example:

docker run -e SLACKEN_MEMORY=32g -p 4040:4040 -v /host/data:/data:rw jnpsolutions/slacken --help

Where: SLACKEN_MEMORY is the amount of RAM you can spare (as much as possible, 32 GB minimum recommended), and

/host/data is a location to use for temporary data on the host (SSD recommended), which must be bound to /data.

Additional arguments on the command line after jnpsolutions/slacken are exactly as if slacken.sh had been invoked directly. For example:

docker run -e SLACKEN_MEMORY=32g -p 4040:4040 -v /host/data:/data:rw jnpsolutions/slacken taxonIndex /data/std_35_31_s7 stats

where std_35_31_s7 is a pre-built index that is located in /host/data on the host.

Please see the GitHub repository linked above for more details on the available commands and a tutorial.

The Spark GUI can be accessed on https://localhost:4040⁠ while Slacken is running.