France's National Gendarmerie – a national law enforcement agency – is now running 37,000 desktop PCs with a custom version of the Linux operating system, and by summer of next year, the agency plans to move all 72,000 of its desktop machines to the open source OS.

Linux is now the primary means of running computer servers inside the data centers that drive the web's biggest services, from Google to Amazon to Facebook, but it has struggled to replace Microsoft Windows on the desktop. The news from the Gendarmerie could be a sign that this is changing.

The agency claims the total cost of ownership of Linux and open source applications is about 40 percent less than proprietary software from Microsoft, according to an article published on the European Union's Interoperability Solutions for Public Administrations website.

To make the switch less abrupt, the Gendarmerie first moved to cross-platform open source applications such as OpenOffice, Firefox, and Thunderbird. That allowed employees to keep using Windows while they got used to the new applications. Only then did the agency move them onto a Linux OS running these same applications.

The migration started in 2004, when the Gendarmerie was faced with providing all its users with access to its internal network. In order to save money, the agency switched from Microsoft Office to OpenOffice. Then the agency rolled out Firefox and Thunderbird in 2006. Finally, in 2008, it switched the first batch of 5,000 users to a Linux OS based on the Ubuntu distribution.

This is one of the largest known government deployments of Linux on the desktop. Many governments, such as Brazil, have resolved to use more open source software. Some countries, like China and India, even have their own government-sponsored Linux distributions. But the actual adoption rate of Linux within government agencies is unclear.

For example, in 2011 the UK government committed to use open source software wherever possible. According to the country's Government Service Design Manual, civil servants are to "use open source software in preference to proprietary or closed source alternatives, in particular for operating systems, networking software, web servers, databases and programming languages." But according to the BBC, the UK government was still spending the majority of its IT budget on proprietary software from companies like Microsoft and Oracle later that year. Part of the problem, according to the BBC, is that agencies are locked into existing proprietary applications.

Another issue is that not all commercial software has a suitable open source replacement, and these proprietary applications might not run on Linux. Multimedia applications such as graphic design, audio engineering, and video editing have particularly lagged on Linux. According to Miguel de Icaza, one of the original designers of the GNOME desktop environment for Linux, the lack of professional applications on Linux has a lot to do with early failures by him and other desktop environment creators to build standardized, backwards-compatible platforms for developers.

There's also the matter of custom applications. Many organizations invested heavily in Windows technologies such as Active X, which only runs on Microsoft's Internet Explorer web browser. For example, the entire country of South Korea – including private enterprises – standardized on Active X in the 1990s, according to the Korea Times. It's expensive and time consuming to rewrite all of this internal code, and since some agencies may depend on Active X-based code from other agencies, they don't necessarily have control over when a migration can take place.

Tools such as virtualization and terminal services can make it possible to run Windows applications on Linux desktops, but this involves purchasing licenses from Microsoft, destroying part of the point of switching to open source operating systems in the first place.

But the growing use of web based applications instead of native desktop applications could make Linux a more viable operating system for not just government agencies, but all large organizations. The Gendarmerie provides a roadmap.