ffmpeg is linux based software that is a bit of a swiss army knife for processing video.

Using PHP to take care of the animated gif assembly, you could easily add in a bit of logic to read a directory and compile gif's from all of the flv's found.

Here is a php code snip for you:
$oMovie = new ffmpeg_movie($inputFile);
$oAnimatedGif = new ffmpeg_animated_gif($outputFile, $width, $height,
$frameRate, $loopCount);
$frame = $oMovie->getNextKeyFrame();
if ($frame) {
$oAnimatedGif->addFrame($frame);
}

Basically, we're using PHP to run ffmpeg, extract a few frames and build the animated gif. Note that ffmpeg must be installed and compiled into php.

PHP can be easily run from the command line.

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