A company called Black Duck Software monitors open source projects to gather stats such as what languages and licenses they use, and how often they release new versions. They currently monitor 180,000 projects on nearly 4,000 sites, and just released some information about the 17,000 new projects which they say were started in 2008.
The stats on language use show a strong lead for C (47%), with Java in second place (28%). However, our interest is caught by the stats for scripting languages, which show that while Javascript is on top with 20%, Perl is close behind it with 18%. Meanwhile PHP was at 11%, and Ruby at 6%.
More information can be found in this press release from Black Duck Software.
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Since many projects, regardless of their language, have a few Perl scripts that do things like automate the build process, I would take the 18% figure for Perl with a big grain of salt.
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