You still need to install the stupidly-named Microsoft Drivers for PHP for SQL Server on your Linux desktop so that PHP on the Linux desktop can connect to your Windows SQL Server computer.
Then run PHPInfo() to confirm that PHP has successfully loaded the MS SQLSRV driver.
Then, when you install Moodle on the Linux desktop you'll be able to select the SQLSRV driver as the driver that Moodle must use to connect to your SQL Server computer.
For info try this link.