Check code out from github. Go into the cestaan directory.
mkdir data source_data scripts/source_data, then copy data there.*
cd scripts and run the create_database.py command. Move the
scripts/data/output.sqlite file to data/output.sqlite.
Check app.py, generate_umap.R, and generate_violin.R and make
sure CESTAAN_ROOT is logical.†
mkdir venv, and then virtualenv venv. Use venv/bin/pip to
install pacages listed in requirements.txt.
To run it first do, in the root cestaan directory do
venv/bin/activate, and then shiny run --port 8070 app.py. Or set
up a system service with a file like:
[Unit]
Description=Start CeSTAAN shiny thingy
[Service]
User=ctvm1
Group=ctvm1
WorkingDirectory=/var/www/cestaan
Environment=BASH_ENV=./venv/bin/activate
ExecStart=/usr/bin/bash -c "shiny run --port 8070 app.py"
[Install]
WantedBy=multi-user.target
The point your browser to port 8070, or set up a web server to proxy to that port.
* Not yet sure where to get the data.
† Should create global config.