| Name | funannotate2 JSON |
| Version |
25.11.1
JSON |
| download |
| home_page | None |
| Summary | Funannotate2: eukarytoic genome annotation pipeline |
| upload_time | 2025-11-02 22:26:16 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7.0 |
| license | BSD 2-Clause License
Copyright (c) 2023, Jon Palmer
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
annotation
bioinformatics
genome
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://github.com/nextgenusfs/funannotate2/releases/latest)
[](https://github.com/psf/black)
[](https://github.com/nextgenusfs/funannotate2/actions/workflows/tests.yml)
# funannotate2: eukaryotic genome annotation pipeline
Funannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating
eukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.
### Quick start: Installation
#### Linux systems
Unit this gets pushed to bioconda, can try this:
```shell
mamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite
conda activate funannotate2
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
```
#### Apple Silicon (M series)
Installation on apple silicon (M series) is a little bit more involved due to some dependency issues and non-native builds of some software. I've not been able to find or build a version of `augustus` that will run, so instead I've been running `augustus` and `genemark` locally with Docker. I've setup two repos with instructions on how to get this working (Need Docker Desktop installed) and then will need to put the bash wrapper files in your PATH to mimic the CLI interface.
https://github.com/nextgenusfs/dockerized-augustus
https://github.com/nextgenusfs/dockerized-genemark
Once that is working, you can then install most of the remaining dependencies with conda, although we need to leave out both `buscolite` and `funannotate2` because they have `augustus` as a dependency, instead we will install those python packages with pip. The conda mkl<2022 is to avoid an annoying warning on apple silicon with the intel mkl package.
```shell
# first install most of the dependencies
mamba create -n funannotate2 --platform osx-64 "python>=3.7,<3.13" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair pytantan "mkl<2022"
# we can then add the required FUNANNOTATE2_DB env variable to the conda environment, note need to reactivate to use it
conda activate funannotate2
conda env config vars set FUNANNOTATE2_DB=/path/to/funannotate2-db
conda env config vars set AUGUSTUS_CONFIG_PATH=/path/to/augustus-3.5.0/config
conda deactivate
# now reactivate environment, and install the remaining python dependencies with pip
conda activate funannotate2
python -m pip install buscolite git+https://github.com/nextgenusfs/funannotate2.git
# now we can install the databases
funannotate2 install -d all
```
#### Other/Manual Installation
Additional tools like genemarkHMM must be installed manually due to licensing.
`funannotate2` is a python package, to install release versions use the pip package manager, like so:
```shell
pip install funannotate2
```
Or to install the bleeding edge version from github repo:
```shell
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
```
## Development
### Testing
Funannotate2 includes both unit tests and integration tests to ensure the code works correctly.
#### Running Tests
To run the tests, you need to install pytest and the package in development mode:
```bash
# Install pytest and coverage tools
pip install pytest pytest-cov
# Install funannotate2 in development mode
pip install -e .
# Run all tests
pytest
# Run with coverage report
pytest --cov=funannotate2
# Generate HTML coverage report
python scripts/run_coverage.py
```
For more information about testing, see the [TESTING.md](TESTING.md) file.
### Development Dependencies
To work on funannotate2 development, you'll need to install the development dependencies:
```shell
pip install pytest pytest-cov
```
### Documentation
Funannotate2 includes comprehensive documentation that covers installation, usage, API reference, and more. To build the documentation:
```bash
# Install Sphinx and the theme
pip install sphinx sphinx_rtd_theme
# Build the documentation
cd docs
make html
```
The built documentation will be in the `docs/_build/html` directory.
For more information about the documentation, see the [docs/README.md](docs/README.md) file.
### Running Tests
After installing the development dependencies, you can run the tests with:
```shell
python -m pytest
```
To run tests with coverage reporting:
```shell
python -m pytest --cov=funannotate2 --cov-report=term-missing
```
Or use the provided script to generate an HTML coverage report:
```shell
python scripts/run_coverage.py
```
To install the most up to date code from this repo, you can run:
```
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git --upgrade --force --no-deps
```
### Citation
Funannotate2 includes a CITATION.cff file that provides citation information for the software. The version and release date in this file are automatically updated when a new release is created.
To cite funannotate2 in your work, you can use the citation information from the CITATION.cff file or generate a citation in your preferred format using tools like [citeas.org](https://citeas.org/).
Raw data
{
"_id": null,
"home_page": null,
"name": "funannotate2",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.7.0",
"maintainer_email": null,
"keywords": "annotation, bioinformatics, genome",
"author": null,
"author_email": "Jon Palmer <nextgenusfs@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/64/7b/c94a617bddac895807aa1938ae390047b96ea3b64159705fbc746eeaa089/funannotate2-25.11.1.tar.gz",
"platform": null,
"description": "[](https://github.com/nextgenusfs/funannotate2/releases/latest)\n\n[](https://github.com/psf/black)\n[](https://github.com/nextgenusfs/funannotate2/actions/workflows/tests.yml)\n\n# funannotate2: eukaryotic genome annotation pipeline\n\nFunannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating\neukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.\n\n\n### Quick start: Installation\n\n#### Linux systems\n\nUnit this gets pushed to bioconda, can try this:\n```shell\nmamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap \"augustus==3.5.0\" glimmerhmm diamond trnascan-se table2asn gb-io buscolite\nconda activate funannotate2\npython -m pip install git+https://github.com/nextgenusfs/funannotate2.git\n```\n\n#### Apple Silicon (M series)\nInstallation on apple silicon (M series) is a little bit more involved due to some dependency issues and non-native builds of some software. I've not been able to find or build a version of `augustus` that will run, so instead I've been running `augustus` and `genemark` locally with Docker. I've setup two repos with instructions on how to get this working (Need Docker Desktop installed) and then will need to put the bash wrapper files in your PATH to mimic the CLI interface.\n\nhttps://github.com/nextgenusfs/dockerized-augustus\n\nhttps://github.com/nextgenusfs/dockerized-genemark\n\nOnce that is working, you can then install most of the remaining dependencies with conda, although we need to leave out both `buscolite` and `funannotate2` because they have `augustus` as a dependency, instead we will install those python packages with pip. The conda mkl<2022 is to avoid an annoying warning on apple silicon with the intel mkl package.\n\n```shell\n# first install most of the dependencies\nmamba create -n funannotate2 --platform osx-64 \"python>=3.7,<3.13\" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair pytantan \"mkl<2022\"\n\n# we can then add the required FUNANNOTATE2_DB env variable to the conda environment, note need to reactivate to use it\nconda activate funannotate2\nconda env config vars set FUNANNOTATE2_DB=/path/to/funannotate2-db\nconda env config vars set AUGUSTUS_CONFIG_PATH=/path/to/augustus-3.5.0/config\nconda deactivate\n\n# now reactivate environment, and install the remaining python dependencies with pip\nconda activate funannotate2\npython -m pip install buscolite git+https://github.com/nextgenusfs/funannotate2.git\n\n# now we can install the databases\nfunannotate2 install -d all\n```\n\n#### Other/Manual Installation\n\nAdditional tools like genemarkHMM must be installed manually due to licensing.\n\n`funannotate2` is a python package, to install release versions use the pip package manager, like so:\n\n```shell\npip install funannotate2\n```\nOr to install the bleeding edge version from github repo:\n\n```shell\npython -m pip install git+https://github.com/nextgenusfs/funannotate2.git\n```\n\n## Development\n\n### Testing\n\nFunannotate2 includes both unit tests and integration tests to ensure the code works correctly.\n\n#### Running Tests\n\nTo run the tests, you need to install pytest and the package in development mode:\n\n```bash\n# Install pytest and coverage tools\npip install pytest pytest-cov\n\n# Install funannotate2 in development mode\npip install -e .\n\n# Run all tests\npytest\n\n# Run with coverage report\npytest --cov=funannotate2\n\n# Generate HTML coverage report\npython scripts/run_coverage.py\n```\n\nFor more information about testing, see the [TESTING.md](TESTING.md) file.\n\n### Development Dependencies\n\nTo work on funannotate2 development, you'll need to install the development dependencies:\n\n```shell\npip install pytest pytest-cov\n```\n\n### Documentation\n\nFunannotate2 includes comprehensive documentation that covers installation, usage, API reference, and more. To build the documentation:\n\n```bash\n# Install Sphinx and the theme\npip install sphinx sphinx_rtd_theme\n\n# Build the documentation\ncd docs\nmake html\n```\n\nThe built documentation will be in the `docs/_build/html` directory.\n\nFor more information about the documentation, see the [docs/README.md](docs/README.md) file.\n\n### Running Tests\n\nAfter installing the development dependencies, you can run the tests with:\n\n```shell\npython -m pytest\n```\n\nTo run tests with coverage reporting:\n\n```shell\npython -m pytest --cov=funannotate2 --cov-report=term-missing\n```\n\nOr use the provided script to generate an HTML coverage report:\n\n```shell\npython scripts/run_coverage.py\n```\n\nTo install the most up to date code from this repo, you can run:\n```\npython -m pip install git+https://github.com/nextgenusfs/funannotate2.git --upgrade --force --no-deps\n```\n\n### Citation\n\nFunannotate2 includes a CITATION.cff file that provides citation information for the software. The version and release date in this file are automatically updated when a new release is created.\n\nTo cite funannotate2 in your work, you can use the citation information from the CITATION.cff file or generate a citation in your preferred format using tools like [citeas.org](https://citeas.org/).\n\n",
"bugtrack_url": null,
"license": "BSD 2-Clause License\n \n Copyright (c) 2023, Jon Palmer\n \n Redistribution and use in source and binary forms, with or without\n modification, are permitted provided that the following conditions are met:\n \n 1. Redistributions of source code must retain the above copyright notice, this\n list of conditions and the following disclaimer.\n \n 2. Redistributions in binary form must reproduce the above copyright notice,\n this list of conditions and the following disclaimer in the documentation\n and/or other materials provided with the distribution.\n \n THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\n AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\n IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\n DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\n FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\n DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\n SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\n CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\n OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\n OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.",
"summary": "Funannotate2: eukarytoic genome annotation pipeline",
"version": "25.11.1",
"project_urls": {
"Homepage": "https://github.com/nextgenusfs/funannotate2",
"Repository": "https://github.com/nextgenusfs/funannotate2.git"
},
"split_keywords": [
"annotation",
" bioinformatics",
" genome"
],
"urls": [
{
"comment_text": null,
"digests": {
"blake2b_256": "53bf50cf1c08f056a405670da7d7429266a0efde4fe4831ea2bd4d85bdcf2311",
"md5": "acc6192c0e87835049d8dc1500545850",
"sha256": "317fbd111b96d17d5086c89793e3c84533918dfaa492e10b8ca92cd8965ad833"
},
"downloads": -1,
"filename": "funannotate2-25.11.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "acc6192c0e87835049d8dc1500545850",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7.0",
"size": 134932,
"upload_time": "2025-11-02T22:26:15",
"upload_time_iso_8601": "2025-11-02T22:26:15.166833Z",
"url": "https://files.pythonhosted.org/packages/53/bf/50cf1c08f056a405670da7d7429266a0efde4fe4831ea2bd4d85bdcf2311/funannotate2-25.11.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": null,
"digests": {
"blake2b_256": "647bc94a617bddac895807aa1938ae390047b96ea3b64159705fbc746eeaa089",
"md5": "a6bfd3f0c2543a6fef4cee981fccce49",
"sha256": "d467f4869997cf650a80d0d4a2442292489daef36aa78d43fc8ddb6dc2bec9f8"
},
"downloads": -1,
"filename": "funannotate2-25.11.1.tar.gz",
"has_sig": false,
"md5_digest": "a6bfd3f0c2543a6fef4cee981fccce49",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7.0",
"size": 121708,
"upload_time": "2025-11-02T22:26:16",
"upload_time_iso_8601": "2025-11-02T22:26:16.784477Z",
"url": "https://files.pythonhosted.org/packages/64/7b/c94a617bddac895807aa1938ae390047b96ea3b64159705fbc746eeaa089/funannotate2-25.11.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2025-11-02 22:26:16",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "nextgenusfs",
"github_project": "funannotate2",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "funannotate2"
}
