Anvi'o 7

2021-08-02 278 words 2 minutes

Anvi’o: integrated multi-omics at scale

Anvi’o is a collection of tools and an interactive viewer that allows for determination and inspection of multi-omic data.

Location and version:

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$ which anvi-interactive
/local/cluster/anvio-7/bin/anvi-interactive
$ anvi-interactive --version
Anvi'o .......................................: hope (v7)

Profile database .............................: 35
Contigs database .............................: 20
Pan database .................................: 14
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 2
tRNA-seq database ............................: 1

To use:

Request a PORT forwarding number so that we don’t have collisions. E-mail me and ask for a PORT number.

You’ll have to use your PORT to access the web browser that will be forwarded through shell.cgrb.oregonstate.edu. This PORT is unrelated to any other PORT used to connect to the infrastructure.

After you get your PORT, you’ll need to modify your ssh command, by adding these flags:

-L <PORT NUMBER>:<NODE ON CLUSTER>:<PORT NUMBER>

Then, when you log in, you will check out the same node (using qrsh) that you specify in your ssh command. You can freely choose any node that you have interactive qrsh access to, but you must use the same node in the -L flag to ssh as you do to qrsh to once inside the network.

To activate the anvio enviroment:

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bash
source /local/cluster/anvio/activate.sh

This will get you an interactive session that will tunnel through the shell.cgrb machine.

To test your setup:

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cp -R /local/cluster/anvio/test-data .
cd test-data
bash ./run.sh

Open your chrome-based browser and navigate to localhost:PORT to see your interactive session.

software ref: https://merenlab.org/software/anvio
research ref: https://merenlab.org/software/anvio/citing
research ref: https://doi.org/10.1038/s41564-020-00834-3