Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
3 of 31 committers (9.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.6%) to scientific vocabulary
Keywords
Repository
Eukaryotic Genome Annotation Pipeline
Basic Info
- Host: GitHub
- Owner: nextgenusfs
- License: bsd-2-clause
- Language: Python
- Default Branch: master
- Homepage: http://funannotate.readthedocs.io
- Size: 32.5 MB
Statistics
- Stars: 361
- Watchers: 17
- Forks: 88
- Open Issues: 291
- Releases: 78
Topics
Metadata Files
README.md
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io
Quickest start Docker:
You can use docker to run funannotate. Caveats are that GeneMark is not included in the docker image (see licensing below and you can complain to the developers for making it difficult to distribute/use). I've also written a bash script that can run the docker image and auto-detect/include the proper user/volume bindings. This docker image is built off of the latest code in master, so it will be ahead of the tagged releases. The image includes the required databases as well, if you want just funannotate without the databases then that is located on docker hub as well nextgenusfs/funannotate-slim. So this route can be achieved with:
```
download/pull the image from docker hub
$ docker pull nextgenusfs/funannotate
download bash wrapper script (optional)
$ wget -O funannotate-docker https://raw.githubusercontent.com/nextgenusfs/funannotate/master/funannotate-docker
might need to make this executable on your system
$ chmod +x /path/to/funannotate-docker
assuming it is in your PATH, now you can run this script as if it were the funannotate executable script
$ funannotate-docker test -t predict --cpus 12 ```
Quickstart Bioconda install:
The pipeline can be installed with conda (via bioconda): ```
add appropriate channels
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
then create environment
conda create -n funannotate "python>=3.6,<3.9" funannotate
If `conda` is taking forever to solve the environment, I would recommend giving [mamba](https://github.com/mamba-org/mamba) a try:
install mamba into base environment
conda install -n base mamba
then use mamba as drop in replacmeent
mamba create -n funannotate funannotate ```
If you want to use GeneMark-ES/ET you will need to install that manually following developers instructions: http://topaz.gatech.edu/GeneMark/license_download.cgi
Note that you will need to change the shebang line for all perl scripts in GeneMark to use /usr/bin/env perl.
You will then also need to add gmes_petap.pl to the $PATH or set the environmental variable $GENEMARKPATH to the gmespetap directory.
To install just the python funannotate package, you can do this with pip:
python -m pip install funannotate
To install the most updated code in master you can run:
python -m pip install git+https://github.com/nextgenusfs/funannotate.git
Citation
Jonathan M. Palmer, & Jason Stajich. (2020). Funannotate v1.8.1: Eukaryotic genome annotation (v1.8). Zenodo. https://doi.org/10.5281/zenodo.1134477
Owner
- Name: Jon Palmer
- Login: nextgenusfs
- Kind: user
- Location: Palo Alto, CA
- Repositories: 9
- Profile: https://github.com/nextgenusfs
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Funannotate
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Jonathan M.
family-names: Palmer
email: nextgenusfs@gmail.com
affiliation: USDA Forest Service
orcid: 'https://orcid.org/0000-0003-0929-3658'
- given-names: Jason E.
family-names: Stajich
email: jason.stajich@ucr.edu
orcid: 'https://orcid.org/0000-0002-7591-0020'
affiliation: University of California-Riverside
identifiers:
- type: url
value: 'https://funannotate.readthedocs.io/'
description: ReadTheDocs documentation
- type: doi
value: 10.5281/zenodo.1134477
description: Zenodo archive of Funannotate software
repository-code: 'https://github.com/nextgenusfs/funannotate'
repository-artifact: 'https://doi.org/10.5281/zenodo.1134477'
abstract: >-
Funannotate is a genome prediction, annotation, and
comparison software package. It was originally written to
annotate fungal genomes (small eukaryotes ~ 30 Mb
genomes), but has evolved over time to accomodate larger
genomes. The impetus for this software package was to be
able to accurately and easily annotate a genome for
submission to NCBI GenBank.
keywords:
- bioinformatics
- genome annotation
- genomics
- gene prediction
license: BSD-2-Clause
version: 1.8.16
date-released: '2023-08-22'
GitHub Events
Total
- Issues event: 60
- Watch event: 35
- Issue comment event: 143
- Push event: 5
- Pull request review event: 1
- Pull request event: 3
- Fork event: 3
Last Year
- Issues event: 60
- Watch event: 35
- Issue comment event: 143
- Push event: 5
- Pull request review event: 1
- Pull request event: 3
- Fork event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jon Palmer | j****n@J****l | 698 |
| Jon Palmer | n****s@g****m | 438 |
| Jason Stajich | j****d@g****m | 99 |
| Jon Palmer | n****s@g****m | 64 |
| CFMR NGS | n****s@C****l | 59 |
| Ion PGM | n****s@n****s | 13 |
| Package Admin | r****t@b****r | 10 |
| Jon Palmer | j****n@c****u | 5 |
| Mark Lubberts | m****r | 5 |
| Jon Palmer | j****n@J****t | 4 |
| IanDMedeiros | 8****s | 4 |
| Daniel Bogema | d****a@d****u | 2 |
| Erik Kastman | e****n@g****m | 2 |
| trvinh | t****h@g****m | 2 |
| Tyler Esser | t****r@u****u | 2 |
| Anthony Bretaudeau | a****u@i****r | 1 |
| David Winter | d****r@g****m | 1 |
| Philipp Resl | r****p@g****m | 1 |
| mikolajdziurzynski | d****m@g****m | 1 |
| mglubber | m****s@g****m | 1 |
| Simonas Marcišauskas | s****c@l****l | 1 |
| Ed Davis | d****v@g****m | 1 |
| Bogdan | t****n@g****m | 1 |
| xvazquezc | x****c | 1 |
| StarSkyZheng | q****5 | 1 |
| Julian Liber | 3****l | 1 |
| Adhemar Zerlotini | a****o@g****m | 1 |
| Jon Palmer | j****n@J****n | 1 |
| Victor de Jager | V****r@b****m | 1 |
| Björn Grüning | b****n@g****u | 1 |
| and 1 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 310
- Total pull requests: 21
- Average time to close issues: about 2 months
- Average time to close pull requests: 4 days
- Total issue authors: 209
- Total pull request authors: 8
- Average comments per issue: 4.1
- Average comments per pull request: 0.48
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 51
- Pull requests: 3
- Average time to close issues: about 1 month
- Average time to close pull requests: about 3 hours
- Issue authors: 42
- Pull request authors: 2
- Average comments per issue: 1.8
- Average comments per pull request: 1.67
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lalalagartija (6)
- DiegoSafian (5)
- hassantarabai (5)
- Nitin123-4 (5)
- JWDebler (4)
- hyphaltip (4)
- caonetto (4)
- xvazquezc (4)
- kushalsuryamohan (4)
- ad010902 (3)
- maysonlin (3)
- maruiqi0710 (3)
- mojiefei (3)
- dgslos (3)
- kalonji08 (3)
Pull Request Authors
- hyphaltip (13)
- photocyte (3)
- tayabsoomro (3)
- feibendepiaoerbai (2)
- IanDMedeiros (2)
- liberjul (1)
- abretaud (1)
- mdziurzynski (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 168 last-month
- Total docker downloads: 734
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 14
- Total maintainers: 1
pypi.org: funannotate
funannotate: eukaryotic genome annotation pipeline
- Homepage: https://github.com/nextgenusfs/funannotate
- Documentation: https://funannotate.readthedocs.io/
- License: BSD-2
-
Latest release: 1.8.17
published about 2 years ago
Rankings
Maintainers (1)
Dependencies
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- docker/build-push-action v2 composite
- docker/login-action v1 composite
- docker/setup-buildx-action v1 composite
- peter-evans/repository-dispatch v1 composite
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- actions/setup-python v2 composite
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- docker/login-action v1 composite
- docker/setup-buildx-action v1 composite
- kaliber5/action-get-release v1 composite
- actions/checkout v2 composite
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- kaliber5/action-get-release v1 composite
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- actions/checkout v1 composite
- chrnorm/deployment-action releases/v1 composite
- chrnorm/deployment-status releases/v1 composite
- actions/checkout v2 composite
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- docker/login-action v1 composite
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- peter-evans/repository-dispatch v1 composite
- continuumio/miniconda3 latest build
- debian buster build