lis-autocontent

Scrapes the LIS datastore (https://data.legumeinfo.org) and populates various configs and databases for deployment

Reqiurements

1. JBrowse2 (https://jbrowse.org/jb2/docs/combined/)
2. NCBI-BLAST+ (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
3. Python3.7+

Quick Install With pip

1. Create a virtual environment for python3. python3 -m venv lis_autocontent_env (optional)
2. Source environment. . ./lis_autocontent_env/bin/activate (optional)
3. pip install from pypi. pip install lis-autocontent

Developer Install

1. Clone repository. git clone https://github.com/legumeinfo/LIS-autocontent.git
2. Create a virtual environment for python3 python3 -m venv lis_autocontent_env (optional)
3. Source virtual environment . ./lis_autocontent_env/bin/activate (optional)
4. CD into repo and install requirements. cd LIS-autocontent/;pip install -r requirements.txt (optional)
5. Install Black and pre-commit for git hooks. pip install black pre-commit
6. Initialize pre-commit (if you haven't already). pre-commit install
7. Build package locally. python setup.py build (optional)
8. 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