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What distro do you use?
I recently needed to install that on Ubuntu, and it was a simple matter of:
apt-get install ffmpeg
And same with the php5 module:
apt-get install php5-ffmpeg
However, even with another distro, it shouldn't cause everything to get screwed up -- what sort of problems do you run into?
-Eric
centos 5
yum doesn't do that unless you have dag in your repos, but you dont want that as dag breaks your webmin.
so best is to check out the website http://ffmpeg.mplayerhq.hu/
i installed ffmpeg which came with the mediaserver and its also included in the gallery2 script.
if in the end you cant do it I suggest to install gallery2, get the ffmpeg through the script and then delete the gallery again, thus leaving the ffmpeg in the correct place