Automated Website Backups with Cron + rclone (S3 / Backblaze B2 / Wasabi)

JetBackup already takes weekly backups of your Domain India hosting account. This guide adds a second, independent copy that you control: a nightly database dump and file archive, encrypted and sent off-site to S3-compatible storage such as Backblaze B2, Wasabi, Cloudflare R2 or Amazon S3, with rclone and a cron job. It works on your own VPS and, with some limits, on shared hosting.

1. Why an off-site copy, when JetBackup exists

On Domain India cPanel and DirectAdmin hosting, JetBackup 5 takes a backup every Sunday and keeps the last 5 copies, and you can restore or download from it yourself (see Backup and Restore with JetBackup). That covers "I deleted something" very well.

An independent copy covers what a provider backup can't:

• Frequency. A weekly copy can be up to a week old. A busy shop or forum may want a nightly database dump.
• History. Five weekly copies reach back about five weeks. A hack noticed late may be older than that.
• Your own control. A copy in your own storage account survives a mistake in your hosting account and is there if you ever move provider.

This follows the familiar 3-2-1 rule: three copies of your data, on two different kinds of storage, with one copy off-site.

2. Choose S3-compatible storage

rclone speaks to all the common providers with the same commands. Compare them on:

• Storage price per GB per month.
• Egress (download) fees, which you pay when you restore. Some providers charge nothing, some include a free allowance.
• Minimum storage duration or minimum monthly charge. Some providers bill deleted files for a minimum number of days, which matters if you prune often.
• Region, if you want the data held in a particular country.

Prices change, so check each provider's current pricing page. For a small site, any of them costs very little.

Create a bucket for backups, and an access key limited to that bucket. Never use your provider's root or account-wide keys on a web server.

3. Install rclone

On your own VPS (root access):

curl https://rclone.org/install.sh | sudo bash
rclone version

On shared hosting, the install script needs root, so it will not work. rclone is a single binary, so you can place it in your home folder over jailed SSH instead:

mkdir -p ~/bin && cd ~/bin
curl -LO https://downloads.rclone.org/rclone-current-linux-amd64.zip
unzip -j rclone-current-linux-amd64.zip '*/rclone' && rm rclone-current-linux-amd64.zip
chmod 700 rclone && ./rclone version

curl, unzip, mysqldump, tar, gzip and crontab are all available inside the jailed shell on our cPanel and DirectAdmin servers. SSH is off by default; ask support to enable it, and see Enabling and accessing jailed SSH. If rclone does not run on your account, pull backups from another machine instead (section 8).

4. Configure the storage and encryption remotes

Run rclone config (or ~/bin/rclone config) and create two remotes:

Everything written to secure: is encrypted on your server before upload, including the file names. The provider only ever sees ciphertext.

5. The backup script

Keep the database password out of the script and out of the process list. Put it in ~/.my.cnf, readable only by you (chmod 600 ~/.my.cnf). If the file already exists, add the section to it:

[mysqldump]
user=youruser_dbuser
password=your-database-password

Then create ~/bin/offsite-backup.sh:

#!/bin/bash
set -euo pipefail
RCLONE="$HOME/bin/rclone"        # or: rclone, on a VPS
DB="youruser_wpdb"
DEST="secure:$(date +%Y/%m)"
STAMP=$(date +%Y%m%d-%H%M)

# 1. Database: streamed, never written to local disk
mysqldump --single-transaction --quick --default-character-set=utf8mb4 "$DB" \
  | gzip | "$RCLONE" rcat "$DEST/db-$STAMP.sql.gz"

# 2. Files: streamed the same way
tar -czf - -C "$HOME" public_html \
  --exclude='public_html/wp-content/cache' \
  | "$RCLONE" rcat "$DEST/files-$STAMP.tar.gz"

# 3. Prune copies older than 30 days
"$RCLONE" delete secure: --min-age 30d

# 4. Optional: tell a monitoring service the run finished
[ -n "${HEARTBEAT_URL:-}" ] && curl -fsS --retry 3 "$HEARTBEAT_URL" >/dev/null
echo "$(date) backup OK"

Make it executable with chmod 700 ~/bin/offsite-backup.sh and run it once by hand.

Streaming with rclone rcat means no temporary archive takes up your disk quota. --single-transaction gives a consistent dump of InnoDB tables without locking your site.

6. Schedule it with cron

Add a line in your control panel's Cron Jobs page, or with crontab -e:

30 2 * * * $HOME/bin/offsite-backup.sh >> $HOME/offsite-backup.log 2>&1

That runs at 2:30 every night. Pick a quiet hour. For the syntax, see the Cron Expression Cheat Sheet.

7. Retention, alerts and restore tests

• Retention: 30 daily copies is enough for most small sites. For longer history, run a second weekly job to a separate folder with a longer --min-age, or use a tool with built-in rotation, such as restic.
• Alerts: a cron job that silently stops is the most common backup failure. A heartbeat service such as Healthchecks.io emails you when the expected ping doesn't arrive. Set HEARTBEAT_URL in the crontab line or the script.
• Restore tests: once a month, download a copy and restore it somewhere harmless, such as a staging subdomain:

rclone copy secure:2026/09/db-20260915-0230.sql.gz .
gunzip -c db-20260915-0230.sql.gz | mysql -u youruser_dbuser -p youruser_stagingdb
rclone cat secure:2026/09/files-20260915-0230.tar.gz | tar -xzf - -C ~/staging

A backup you have never restored is only a hope.

8. Other ways to do it

• Pull instead of push. From a VPS or your own computer, copy the files over SFTP or scp, or tar over SSH, and dump the database through an SSH tunnel. rsync is not available in the shared hosting jail.
• restic or Borg give encrypted, deduplicated snapshots with rotation built in. They suit a VPS well.
• Download from JetBackup now and then, and store the archive yourself.

9. Running this on Domain India

Domain India shared hosting includes JetBackup weekly backups; we don't sell a separate backup add-on. If you need a server you control fully, for this and more, see VPS plans.

Prices on the cards exclude 18% GST.

Ready to set it up? Read Backup and Restore with JetBackup for the backups you already have, ask for jailed SSH, or compare VPS plans if you want full control.