anvi-setup-trna-taxonomy

Authors
Requires
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

The purpose of this program is to setup necessary databases for tRNA genes collected from GTDB (https://gtdb.ecogenomic.org/), genomes in your local anvi'o installation so taxonomy information for a given set of tRNA sequences can be identified using anvi-run-trna-taxonomy and made sense of via anvi-estimate-trna-taxonomy).

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Authors

A. Murat Eren (Meren)

Requires

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

Provides

trna-taxonomy-db

Usage

This program downloads a local copy of a subset of the databases from GTDB (stored in a trna-taxonomy-db), so that tRNA sequences in your dataset can be associated with taxonomy information. It is required to run this program before you can run anvi-run-trna-taxonomy or anvi-estimate-trna-taxonomy.

Like other anvi-setup- programs, this only needs to be run once per anvi’o version. The default path is anvio/data/misc/TRNA-TAXONOMY. You can store the resulting trna-taxonomy-db in a custom location if desired), but then you’ll need to provide the path to it whenever you run anvi-run-trna-taxonomy.

To run this program, you can simply run

anvi-setup-trna-taxonomy

If you are trying to redownload these databases, run:

anvi-setup-trna-taxonomy --reset

Alternatively, you can use --redo-databases if you just want to update the database version without redownloading the data.

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-trna-taxonomy.

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-trna-taxonomy [-h] [-T NUM_THREADS] [--trna-taxonomy-data-dir PATH] [--reset] [--redo-databases]

Parameters and their descriptions

options

-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
--trna-taxonomy-data-dir PATH: The directory for tRNA taxonomy data to be stored (or read from, depending on the context). If you leave it as is without specifying anything, anvi'o will set up everything in (or try to read things from) 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 databases. If you are using a program (such as `anvi-run-trna-taxonomy` or `anvi-estimate-trna-taxonomy`) you will have to use this parameter to tell those programs where your data are.
--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.
--redo-databases: Remove existing databases and re-create them. This can be necessary when versions of programs change and databases they create and use become incompatible.

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.