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wtmatlock / flanker

Gene-flank analysis tool
MIT License
26 stars 8 forks source link

Packaging and testing #21

Closed bede closed 3 years ago

bede commented 3 years ago

Hi guys, useful tool! Will sent me an example CTX-M and I managed to get it working. I assume you're intending to release this, so moved things into a package structure and added a basic test of the CLI running the CTX-M example Will shared.

I've updated the readme, but basically the way to install this packaged branch is:

conda create -n flanker python=3 abricate biopython mash  # needs bioconda channel
# download package tarball
pip install --editable /path/to/flanker/package

You should also be able to pip install directly from GitHub assuming you are authenticated


pip install git+https://github.com/bede/flanker.git@packaging-tests
bede commented 3 years ago

Another consequence is that rather than flanker.py, the command line entry point is now just flanker

bede commented 3 years ago

It's not a one line install with pip because Abricate has a gazillion Perl dependencies handled by conda. Would therefore strongly suggest releasing as a bionconda package eventually.