Backend Installation

micromamba env create -f environment.yml
micromamba activate celvox_env

In the R console, you can then install the R packages using:

install.packages("fst")

#install.packages("devtools")
devtools::install_github("eonurk/seAMLess")
devtools::install_github("eonurk/seAMLessData")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sva")

# Install MuSiC package
# TODO: This is an old version of the MuSiC package. We need to update it.
install.packages("MCMCpack")
install.packages("nnls")
install.packages("MuSiC", repos = "https://eonurk.github.io/drat/")

Frontend Deployment (celvox.co)

Nginx serves the frontend from /var/www/celvox with SPA fallback to index.html. After pulling latest changes and building, deploy the contents of vite-project/dist to that web root.

One-liner redeploy

cd /root/celvox.co/vite-project \
  && npm ci \
  && npm run build \
  && rsync -av --delete dist/ /var/www/celvox/ \
  && chown -R www-data:www-data /var/www/celvox \
  && find /var/www/celvox -type d -exec chmod 755 {} \; \
  && find /var/www/celvox -type f -exec chmod 644 {} \; \
  && nginx -t \
  && systemctl reload nginx

Optional: backup current site before syncing

ts=$(date +%Y%m%d_%H%M%S); tar -C /var/www -czf /var/www/celvox_${ts}.tgz celvox

Quick check

curl -I https://celvox.co

Notes:

• Update paths if project location or Nginx root changes.
• API requests are proxied under /api to http://127.0.0.1:3001/ per /etc/nginx/sites-available/celvox.co.