ILRI Research Computing

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====== halcyon ======

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

===== Information =====

  * Version: 0.1.1 (note that the [[https://github.com/relastle/halcyon/issues/3|version on GitHub and PyPi doesn't match]])
  * Added: August, 2021
  * Link: https://github.com/relastle/halcyon

===== Usage =====

See which versions of halcyon are available:
<code>$ module avail halcyon</code>

Load one version into your environment and run it:
<code>$ module load halcyon/0.1.1
$ halcyon</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ 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</code>