Installation instruction

as of Nov 2020; will be cleaned up in the future

Docker

• Install Docker
  • Enable running docker without sudo (if running on lab server, ask Loren to add you to the docker group)
  • test with: docker run --rm hello-world

Database access

• Ask Loren for access to lmf-db.cin.ucsf.edu server, where the Datajoint database lives

Create a conda environment

• conda env create --name nwb_datajoint python==3.8

From Anaconda / PyPI:

• Install nodejs
  • conda install -c conda-forge nodejs
• Install jupyterlab
  • conda install -c conda-forge jupyterlab
• Install hither
  • pip install hither
• install spikeinterface
  • pip install spikeinterface
• Install ml_ms4alg
  • pip install ml_ms4alg
• Install datajoint
  • pip install datajoint
  • Change your password for accessing datajoint database and set up external stores

From GitHub:

• Install LorenFrankLab/nwb_datajoint
  • python setup.py develop
• Install NovelaNeuro/ndx-franklab-novela
• Install Labbox-ephys
  • setup.py is in the python subfolder

Notes

• Add environment variables (e.g. in ~/.bashrc)
  • export LABBOX_EPHYS_DATA_DIR="/stelmo/nwb/"
  • export NWB_DATAJOINT_BASE_DIR="/stelmo/nwb/"
  • export KACHERY_STORAGE_DIR="/stelmo/nwb/kachery-storage"
  • export KACHERY_P2P_API_PORT="some-port-number"
  • export KACHERY_P2P_CONFIG_DIR="/your-home-directory/.kachery-p2p"
  • export DJ_SUPPORT_FILEPATH_MANAGEMENT=true

Troubleshooting common problems

• If cannot connect to dj, then downgrade pymysql to 0.9.2
• If cannot write nwb, then downgrade h5py to 2.10.0
• If stall during spikesorting, then install ml_ms4alg from our fork and upgrade numpy to 1.19.4
• If cannot get waveforms, downgrade following packages to these versions:
  spikecomparison 0.3.0 pypi_0 pypi
  spikeextractors 0.9.1 pypi_0 pypi
  spikefeatures 0.1.1 pypi_0 pypi
  spikeinterface 0.10.0 pypi_0 pypi
  spikemetrics 0.2.2 pypi_0 pypi
  spikesorters 0.4.2 pypi_0 pypi
  spiketoolkit 0.7.0 pypi_0 pypi
  spikewidgets 0.5.0 pypi_0 pypi