SciOps Demo Workflow Docker[Legacy]

Drew Yang @ DataJoint | 2021.10.05

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Now this repo is included in SciOps Demo Workflow

Prerequisite

Build the base MATLAB image at first.

• Installer has to be an offline installer that includes all the toolboxes
• Wasn't ablt to activate licenses using the activation binary, but was able to directly mount license file in ~/MATLAB/licenses/ and skip the activation.

The required image is referenced from MATLAB image - Raphael Guzman

.env file exmaple

# MATLAB
MATLAB_HOSTID=06:a4:03:05:48:0c # MAC Address supplied to Mathworks as HostID associated with license.
MATLAB_USER=muser # System/ComputerLogin user associated with license. Default is muser.
MATLAB_UID=1000 # UID of your docker host. This is utilized to resolve permissions on volume data.
MATLAB_GID=1000 # GID of your docker host. This is utilized to resolve permissions on volume data.
MATLAB_IMAGE_TYPE=GUI # Available MATLAB Image types are: GUI, MIN
# MATLAB_LICENSE=$(base64 ./licenses/R2021a_joseph_license.lic -w 0) # base64 encode
MATLAB_VERSION=R2021a # Matlab version to be built. Must supply COMPLETE matlab_RXXXXX_glnxa64.zip for install in an installers dir.
MATLAB_FILE_KEY=<FILEKEY> # Mathworks provided file key associated with installation.
PY_VERSION=3.7 # >= 3.0. Necessary to complete install of Jupyter Notebook with MATLAB kernel (GUI).
MATLAB_INSTALLED_ROOT=/home/muser/.MATLAB # Directory where MATLAB root path is located.

# Datajoint
DJ_HOST=tutorial-db.datajoint.io
DJ_USER=<USERNAME>
DJ_PASS=<PASSWORD>
DATABASE_PREFIX=<USERNAME>_

# Data Input/Output -> Local Mapping
ROOT_DATA_DIR=/mnt/efs-sciops/<USERNAME>/inbox
PROCESSED_DATA_DIR=/mnt/efs-sciops/<USERNAME>/outbox

# In-container Module Directories
ecephys_directory=/home/muser/neuropixel/ecephys_spike_sorting/ecephys_spike_sorting
kilosort_repository=/home/muser/neuropixel/Kilosort-2.5
npy_matlab_repository=/home/muser/neuropixel/npy-matlab
catGTPath=/home/muser/neuropixel/CatGT-linux
tPrime_path=/home/muser/neuropixel/TPrime-linux
cWaves_path=/home/muser/neuropixel/C_Waves-linux
kilosort_output_tmp=/home/muser/neuropixel/data_for_ecephys/kilosort_datatemp

# Workflow worker
WORKER_COUNT=1