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https://github.com/jlsteenwyk/biokit
a versatile toolkit for processing and analyzing diverse types of sequence data
https://github.com/jlsteenwyk/biokit
bioinformatics comparative-genomics evolution evolutionary-biology evolutionary-genomics genomics python
Last synced: 5 days ago
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a versatile toolkit for processing and analyzing diverse types of sequence data
- Host: GitHub
- URL: https://github.com/jlsteenwyk/biokit
- Owner: JLSteenwyk
- License: mit
- Created: 2021-08-04T17:52:44.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-06-12T18:51:43.000Z (5 months ago)
- Last Synced: 2024-10-18T14:13:05.370Z (about 1 month ago)
- Topics: bioinformatics, comparative-genomics, evolution, evolutionary-biology, evolutionary-genomics, genomics, python
- Language: Python
- Homepage: https://jlsteenwyk.com/BioKIT/
- Size: 40.7 MB
- Stars: 21
- Watchers: 3
- Forks: 10
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: change_log.txt
- License: LICENSE.md
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BioKIT is a UNIX shell toolkit for processing molecular sequence data.
If you found biokit useful, please cite the following: *BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data*. Genetics. doi: [10.1101/2021.10.02.462868](https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac079/6583183).
---
This documentation covers downloading and installing BioKIT. Details about each function as well as tutorials for using BioKIT are available in the online documentation.
**Installation**
**If you are having trouble installing BioKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**
To install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
```shell
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install biokit
pip install jlsteenwyk-biokit
```
**Note, the virtual environment must be activated to use biokit.**
After using biokit, you may wish to deactivate your virtual environment and can do so using the following command:
```shell
# deactivate virtual environment
deactivate
```
Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
```shell
# download
git clone https://github.com/JLSteenwyk/BioKIT.git
cd biokit/
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install
make install
```
To deactivate your virtual environment, use the following command:
```shell
# deactivate virtual environment
deactivate
```
**Note, the virtual environment must be activated to use biokit.**
To install via anaconda, execute the following command:
```shell
conda install -c jlsteenwyk jlsteenwyk-biokit
```
Visit here for more information:
https://anaconda.org/JLSteenwyk/jlsteenwyk-biokit
To test biokit installation, launch the help message
```shell
biokit -h
```