anvi-display-pan-graph

Authors
Requires
Provides
Can provide
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Start an anvi'o interactive interface to view pan graphs..

🔙 To the main page of anvi’o programs and artifacts.

Authors

Alexander Henoch

A. Murat Eren (Meren)

Requires

pan-graph-db

Provides

interactive

Can provide

svg

Usage

No one has described the usage of this program :/ If you would like to contribute, please see previous examples here, and feel free to add a Markdown formatted file in that directory named “anvi-display-pan-graph.md”. For a template, you can use the markdown file for anvi-gen-contigs-database. THANK YOU!

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-display-pan-graph.

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-display-pan-graph [-h] [-p PAN_GRAPH_DB] [-g GENOMES_STORAGE] [--dry-run] [-I IP_ADDR] [-P INT] [--browser-path PATH] [--server-only] [--password-protected] [--export-svg FILE_PATH]

Parameters and their descriptions

PRIMARY INPUT Specify where your pan-db is.

-p, --pan-graph-db PAN_GRAPH_DB: Anvi'o pangenome graph database.
-g, --genomes-storage GENOMES_STORAGE: Anvi'o genomes storage file

SERVER CONFIGURATION For power users.

--dry-run: Don't do anything real. Test everything, and stop right before wherever the developer said 'well, this is enough testing', and decided to print out results.
-I, --ip-address IP_ADDR: IP address for the HTTP server. The default ip address (localhost) should work just fine for most. Default: localhost
-P, --port-number INT: Port number to use for anvi'o services. If nothing is declared, anvi'o will try to find a suitable port number, starting from the default port number, 8080.
--browser-path PATH: By default, anvi'o will use your default browser to launch the interactive interface. If you would like to use something else than your system default, you can provide a full path for an alternative browser using this parameter, and hope for the best. For instance we are using this parameter to call Google's experimental browser, Canary, which performs better with demanding visualizations.
--server-only: The default behavior is to start the local server, and fire up a browser that connects to the server. If you have other plans, and want to start the server without calling the browser, this is the flag you need.
--password-protected: If this flag is set, command line tool will ask you to enter a password and interactive interface will be only accessible after entering same password. This option is recommended for shared machines like clusters or shared networks where computers are not isolated.
--export-svg FILE_PATH: The SVG output file path.

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.