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I am running a Ubuntu Server with Windows XP Clients. I have shared files with XP clients via samba share. The problem is there is a huge number of viruses in the share. Is there any way to remove those virus from Ubuntu itself? Windows clients only have read permission.

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You can remove the 'viruses' by logging into the Ubuntu Server command line in front of the actual server or via ssh if enabled. Navigate to the share from the command line and then remove the relevant viruses. Do you need assistance doing this? – kingmilo Jun 3 '13 at 14:56
Could you run something like clamav on it? – brim4brim Jun 3 '13 at 16:04
up vote 5 down vote accepted

Install one of the many available anti-virus tools for Linux: ClamAV, Avast, BitDefender, for example will do just fine and scan the shared files in the Samba shares.

ClamAV for instance has a CLI and a GUI interface, so you can scan a mount point with it via ssh or by getting direct access to the server, no need for an actual graphical interface.
You would then use the command sudo clamscan -r -l /tmp/scan.log /shares to scan recursively the folder /shares and save a log of that scan to /tmp/scan.log.

Don't forget to make a backup of those files before actually running the scanner, some customers won't understand that some files are so infected that there is no recovery for them and the solution will be to just delete them, so before running a scan make sure that in the eventuality of that happening you can serve them in another media so they can take care of it themselves.

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