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Project description
lis-autocontent
Scrapes the LIS datastore (https://data.legumeinfo.org) and populates various configs and databases for deployment
Reqiurements
- JBrowse2 (https://jbrowse.org/jb2/docs/combined/)
- NCBI-BLAST+ (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
- Python3.7+
Quick Install With pip
- Create a virtual environment for python3.
python3 -m venv lis_autocontent_env
(optional) - Source environment.
. ./lis_autocontent_env/bin/activate
(optional) - pip install from pypi.
pip install lis-autocontent
Developer Install
- Clone repository.
git clone https://github.com/legumeinfo/LIS-autocontent.git
- Create a virtual environment for python3
python3 -m venv lis_autocontent_env
(optional) - Source virtual environment
. ./lis_autocontent_env/bin/activate
(optional) - CD into repo and install requirements.
cd LIS-autocontent/;pip install -r requirements.txt
(optional) - Install Black and pre-commit for git hooks.
pip install black pre-commit
- Initialize pre-commit (if you haven't already).
pre-commit install
- Build package locally.
python setup.py build
(optional) - Install package into env and add to PATH.
python setup.py install
(optional)
Run
(lis_autocontent_env) $ lis-autocontent --help
Usage: lis-autocontent [OPTIONS] COMMAND [ARGS]...
Click Group Object to Attach Commands.
Options:
--help Show this message and exit.
Commands:
populate-blast CLI entry for populate-blast
populate-dscensor CLI entry for populate-dscensor
populate-jbrowse2 CLI entry for populate-jbrowse2
populate-jekyll CLI entry for populate-jekyll
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