labsyspharm/minerva-cli repository overview

python minerva.py

# Replace <REPOSITORY> with a repository name, and <DIRECTORY> with a path to a directory.
# All images from the directory and its subdirectories will be imported.

python minerva.py import -r <REPOSITORY> -d <DIRECTORY>

# Log in O2 with SSH
# Clone the minerva-cli repository
git clone https://github.com/labsyspharm/minerva-cli.git

# Load necessary modules (you may need to restart bash shell after running this the first time)
module load conda2

# Create conda environment
conda create --name minerva python=3.6
conda activate minerva
pip install -r requirements.txt

# Configure minerva.config
cp .minerva.example ~/.minerva
# Edit the values in config file
nano minerva.config
# It's a good idea to prevent other users from reading your configuration file
chmod 700 ~/.minerva

# Log in O2 transfer node with SSH (replace ecommonsid with your eCommons user id)
ssh [email protected]
# Copy images from ImStor to scratch space, e.g.
mkdir -p /n/scratch3/$USER/dataset
cp /n/files/ImStor/.../image.ome.tif /n/scratch3/$USER/dataset

# Log in O2 with SSH
ssh [email protected]
# Start interactive O2 session
srun --pty -p interactive --mem 500M -t 0-06:00 /bin/bash

# Activate conda environment
conda activate minerva

# Run Minerva import
# (replace [REPOSITORY] with a repository name)
# All the images from the given directory will be imported
python $HOME/minerva-cli/minerva.py import -r [REPOSITORY] -d /n/scratch3/$USER/dataset

# The following command will export and save the image by its default name, and save only
# the highest pyramid level.
python minerva.py export --id [IMAGE_UUID]