anvi-self-test
A program for anvi'o to test itself.
🔙 To the main page of anvi’o programs and artifacts.
Authors
Requires
This program seems to know what its doing. It needs no input material from its user. Good program.
Provides
This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.
Usage
This program enables an anvi’o user to run component tests on various anvi’o functionality to ensure they are working on their system.
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-self-test.
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-self-test [-h] [--suite SUITE] [-o DIR_PATH] [--no-interactive] [-T NUM_THREADS]
Parameters and their descriptions
--suite SUITE- A suite of component tests to execute. By default this program will execute the mini test of anvi'o, which will help you to see if your computer and installation is able to perform some of the most basic anvi'o operations, such as generating an anvi'o contigs database, profiling BAM files, or starting an interactive interface. But you are welcome to execute different component tests. Here is a list of what is available to you: 'mini', 'metagenomics-full', 'pangenomics', 'pangenome-graphs', 'interactive-interface', 'metabolism', 'reaction-network', 'metabolic-exchanges', 'kegg-mapping', 'display-functions', 'trnaseq', 'inversions', 'process-genbank', 'workflow-contigs', 'workflow-metagenomics', 'workflow-metagenomics-sra', 'workflow-pangenomics', 'workflow-phylogenomics', 'workflow-ecophylo', 'database-migrations', 'workflow-sra-download', 'run-cazymes', 'export-locus' Default:
mini
-o, --output-dir DIR_PATH- If you declare an output dir, all your data will be stored in there, instead of being stored in a temporary directory to be deleted once the tests are done. This is particularly useful if you wish to play with general anvi'o output files
--no-interactive- Don't show anything interactive (if possible).
-T, --num-threads NUM_THREADS- Maximum number of threads to use for multithreading whenever possible. Very conservatively, the default is 1, unless the environmental variable `ANVIO_THREADS` sets another positive integer. If you use this parameter, it will override `ANVIO_THREADS`. It is a good idea to not exceed the number of CPUs / cores on your system. Plus, please be careful with this option if you are running your commands on a SGE -- if you are clusterizing your runs, and asking for multiple threads to use, you may deplete your resources very fast. Default:
1
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.
