An accurate basecaller exploiting an encoder-decoder model with monotonic attention.

• Version: 0.1.1 (note that the version on GitHub and PyPi doesn't match)
• Added: August, 2021
• Link: https://github.com/relastle/halcyon

See which versions of halcyon are available:

$ module avail halcyon

Load one version into your environment and run it:

$ module load halcyon/0.1.1
$ halcyon

Notes from the sysadmin during installation:

$ cd /tmp
$ module load python/3.7
$ sudo mkdir -p /export/apps/halcyon/0.1.1
$ sudo chown aorth /export/apps/halcyon/0.1.1
$ python -m venv /export/apps/halcyon/0.1.1
$ source /export/apps/halcyon/0.1.1/bin/activate
$ pip install --upgrade setuptools pip
$ pip install pyhalcyon
$ sudo chown -R root:root /export/apps/halcyon/0.1.1