How to set up a malware scanner with LMD Maldet and ClamAV on a RunCloud server instance.

One of the popular and open source malware scanners is an app called Linux Malware Detect and works well scanning any Linux web server, it keeps a daily updated database of known malware exploits from an updated registry of which it scans against.

The Linux Malware Detect tool can also integrate with Clam AV Scanner which can speed up file scanning.

How to install Linux Malware Detect

SSH into your server as the root user and cd to /root


Extract It

tar -xvf maldetect-current.tar.gz

Remove the Archive

rm maldetect-current.tar.gz

Move in and Run the Installer

cd maldetect-1.6.4/

… this will download the latest hash registry databases, the installation adds maldetect to /usr/local/ …. now to configure

Configure Linux Malware Detect

Using nano…

nano /usr/local/maldetect/conf.maldet

Set up Email Alerts


# The default email alert toggle

# [0 = disabled, 1 = enabled]


# The subject line for email 
email_subj="maldet alert from $(hostname)"

# The destination addresses for email alerts

# [ values are comma (,) spaced ]


For the email alert swap the email_alert toggle to 1, adjust the subject line email_subj if desired, add in your email address email_addr.

In order for email alerts to work you will need the postfix app on the server configured to send outgoing emails.

Manual Malware Scans On RunCloud Webapps

You can run a manual scan for a user account on a specific webapp or on all webapps :

maldet -a /home/runcloud/webapps/<webapp_name>/

Or all webapps belonging to the same user,  using a wildcard – ?:

maldet -a /home/runcloud/webapps/?/

Or on all users and webapps using multiple wildcards

maldet -a /home/?/webapps/?/

Automatic Daily Malware Scans

When installed LMD (Linux Malware Detect) adds a cron job to the daily folder:


This cron job will update the malware registry it initially downloaded including any new malware threats and also scan all home directories on the server. If anything is found you will get an email about it telling you the path to the offending file.

The cron has a number of webroot paths for popular control panels but RunClouds does not fit in with one of the existing paths so you need to add it into the cron file script, open the cron file

nano /etc/cron.daily/maldet

Find the else statement below and add in the webroot path /home/?/webapps/?/ in…

# cpanel, interworx and other standard home/user/public_html setups

	        $inspath/maldet -b -r /home?/?/public_html/,/var/www/html/,/usr/local/apache/htdocs/,/home/?/webapps/?/ $scan_days >> /dev/null 2>&1

Dealing With Malware Files

Once (…if) you get a file hit on malware you can access your webserver and open the file and clean the malware code out. Then progress to how it got in in the first place – software patching, updating passwords etc

You can also opt to have LMD quarantine any file it finds – this is done back in the config file conf.maldet under the Email Alert section:


# The default quarantine action for malware hits

# [0 = alert only, 1 = move to quarantine & alert]


# Try to clean string based malware injections

# [NOTE: quar_hits=1 required]

# [0 = disabled, 1 = clean]


The default is just to alert, but you can opt to remove the file from the filing system and have LMD also try and remove the malware code – then you just need to inspect and restore the file.

Maldet Log

You can check all maldet activity with the log command which will show you any latest scans and maldet updates, run it…

maldet –log

For a scan report, you can email it, in the log it appears as…

{scan} scan report saved, to view run: maldet --report 200618-0628.16436

Email it…

maldet --report 200618-0628.16436

Further Options

Check further usage with:

maldet --help

or official documentation

Adding ClamAV

You can use the ClamAV as the scanner engine which speeds up the scanning process a lot but it will consume the cpu and memory resources whilst running but this reduces over days as less files are scanned if not modified.

I would recommend not using it on a busy server with less than 3GB of ram, each case may be different, you can always try and see the results with a top command while and if too much resources you can remove it.

Setting up Clam AV

apt-get install clamav clamav-daemon

This will install ClamAV and put it here…


The above directory is where LMD will look for the Clamscan binary and use it when it scans the file system

Remove LMD and Clam AV

If you want to remove these apps…

To remove ClamAV

apt-get remove clamav

To Remove Maldet LMD – run the uninstall script…


More info on LMD


  1. Peter on July 28, 2020 at 3:21 pm


    Thanks for the great tutorial but the Code seems to be a little screwed up, als it is missing line breaks en shows in one line.

    • Neil Gowran on July 30, 2020 at 12:18 am

      Thanks for letting me know – updated.

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