/merino

Pre-publication data flow for PRISM multiplex cell viability assay

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Merino - !! Pre-publication !!

Pre-publication version of data Flow for converting raw PR500 data into processed results

Setting up the environment for development:

  1. Create a local conda environment
    1. <path to conda bin>/conda create --name merino python=2.7.11 numpy=1.11.2 pandas=0.18 h5py=2.6.0 requests==2.13.0 cmappy scipy setuptools
  2. Activate the environment:
    1. source <path to conda bin>/activate merino
  3. Add the merino code directory to the python path:
    1. cd <directory above path to merino code>
    2. python <path to merino code>/setup_merino.py develop
  4. Run tests to verify setup
    1. cd <path to merino code>
    2. for a in test_*.py; do python $a; echo $a; read; done

TODO's

  1. fix broken test: test_assemble_no_davepool.py test_main
  2. get environment working with mysql / caldaia / lims to register plates