Installation
pip install taxaforge
Usage
taxaforge --help
To create standard Kraken2 database
taxaforge build --db-type standard
Before creating a standard database, you can try a smaller database like fungi.
taxaforge build --db-type fungi
To build a ganon2 database instead, pass --tool ganon2
taxaforge build --tool ganon2 --db-type fungi
To use locally downloaded files, run the following command
taxaforge build --db-name k2_test --genomes-dir /path/to/genomes --taxonomy-dir /path/to/taxonomy
To limit the number of genomes in the database, use the --limit option
taxaforge build --db-name k2_test_100 --genomes-dir /path/to/genomes --limit 1000
Config
Read/write config, stored in the OS default config location (~/.config/taxaforge/config.ini on Linux, ~/Library/Application Support/taxaforge/config.ini on macOS).
taxaforge config set threads 8
taxaforge config get threads
taxaforge config
Why TaxaForge?
TaxaForge aims to provide a simple and easy to use tool to build wide variety of taxonomic classifier databases with a single command.
Why not kraken2-build/ganon directly?
kraken2-build and ganon each build databases for their own tool only. TaxaForge wraps the shared download/taxonomy pipeline once and dispatches to the right tool via --tool, so adding support for more classifiers is a matter of plugging in a new build step.
Documentation
1 maintainer
Metadata
1 maintainer
Release files for taxaforge 0.2.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| taxaforge-0.2.2.tar.gz | 13.5 kB | Without provenance | Details for taxaforge-0.2.2.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| taxaforge-0.2.2-py3-none-any.whl | Python 3 | none | any | Details for taxaforge-0.2.2-py3-none-any.whl |
Total release size: 26.6 kB
Release files / taxaforge-0.2.2.tar.gz
| Download URL | taxaforge-0.2.2.tar.gz |
|---|---|
| Size | 13.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
73aa21e3c6fc8c462161cc7f3dabc55b728083768a7ea5a334d431a229cdc9f0
|
|
BLAKE2b-256 checksum How to use checksums |
87624f665c2d872a6febbda94418b48ef563e253d969db58949d87c985e8d38e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.12.13 {"installer":{"name":"uv","version":"0.12.13","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"macOS","version":null,"id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}
|
Release files / taxaforge-0.2.2-py3-none-any.whl
| Download URL | taxaforge-0.2.2-py3-none-any.whl |
|---|---|
| Size | 13.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
162d6886b1cd809fbedf3c9113dece5f8b689bbb42934af4266beab4370ebd70
|
|
BLAKE2b-256 checksum How to use checksums |
4b7f31b4c1e4da2e42fb0014f9730a569f8fa5fb3345dedc484e028c8554c007
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
uv/0.12.13 {"installer":{"name":"uv","version":"0.12.13","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"macOS","version":null,"id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}
|
Security for taxaforge 0.2.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
