anvi-setup-interacdome

Setup InteracDome data.

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Authors

Evan Kiefl
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Requires

This program seems to know what its doing. It needs no input material from its user. Good program.

Provides

interacdome-data

Usage

This program (much like all of the other programs that begin with anvi-setup) sets up a local copy of the InteracDome database for anvi-run-interacdome as well as a local copy of Pfam v31.0, which is what InteracDome is defined for. Note that anvi’o only needs this program to be run once.

Specifically, this downloads InteracDome’s tab-separated files and the Pfam v31.0 HMM profiles for the Pfams in your InteracDome data. This data is stored in the interacdome-data artifact.

It’s easy as 1-2-3:

anvi-setup-interacdome

When running this program, you can provide a path to store your InteracDome data in. The default path is anvio/data/misc/InteracDome; if you use a custom path, you will have to provide it to anvi-run-interacdome with the same parameter. Here is an example run:

anvi-setup-interacdome --interacdome-data-dir path/to/directory

If you want to overwrite any data that you have already downloaded (for example if you suspect something went wrong in the download), add the --reset flag:

anvi-setup-interacdome --interacdome-data-dir path/to/directory \ --reset

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-setup-interacdome.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-setup-interacdome [-h] [--interacdome-data-dir PATH] [--reset]

Parameters and their descriptions

options
--interacdome-data-dir PATH
The path for the interacdome data to be stored. If you leave it as is without specifying anything, anvi'o will set up everything in a pre-defined default directory. The advantage of using the default directory at the time of set up is that every user of anvi'o on a computer system will be using a single data directory, but then you may need to run the setup program with superuser privileges. If you don't have superuser privileges, then you can use this parameter to tell anvi'o the location you wish to use to setup your data.
--reset
Remove all the previously stored files and start over. If something is feels wrong for some reason and if you believe re-downloading files and setting them up could address the issue, this is the flag that will tell anvi'o to act like a real computer scientist challenged with a computational problem.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.

Copyleft, The anvi'o Project