evanroyrees / automappa

An interactive interface for exploration of highly complex metagenomes

Automappa: An interactive interface for exploration of metagenomes

Image Name	Image Tag	Status	Size
evanrees/automappa	main,latest

automappa-demo.mp4

You may also see each page as a static view

🌳 Automappa testing setup/run commands

• Clone the Automappa Repo
• Run make build using Makefile
• Run make up using Makefile
• Open the Automappa url
• Download test data

Miscellaneous

• Using Automappa on a remote server

clone the Automappa Repository

git clone https://github.com/WiscEvan/Automappa

build images for services used by Automappa

make build

build and run automappa services

You can skip make build if you’d like, as this command will build and pull any images not available.

make up

NOTE: If your computer is already using most of its resources, you may need to close some applications so docker may construct all of the necessary Automappa services

Navigate to Automappa page

Once you see automappa_web_1 running from the terminal logs, you should be able to navigate to localhost:8050 🥳

Download Test Data

Test data to try out Automappa may be downloaded from the google drive in the Automappa test data folder

Try out different settings and perform your own refinements on some of this sponge data!

NOTE: This dataset was retrieved from:

Uppal, Siddharth, Jackie L. Metz, René K. M. Xavier, Keshav Kumar Nepal, Dongbo Xu, Guojun Wang, and Jason C. Kwan. 2022. “Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics.” mBio 13 (5): e0152422.

Happy binning!

Contributors