I've found many downloadeable software to do this, bu I just wanted to do it in the minimalistic way....

These two scripts can be run from a linux terminal or from a. sh file and will convert all the .flac files in the current directory to .ogg or .mp3

for i in *.flac; do
 echo Creating ${i%*.flac}.ogg
 gst-launch-0.10 filesrc location="$i" ! decodebin ! audioconvert !  vorbisenc ! oggmux ! filesink location="${i%*.flac}.ogg"
done

for i in *.flac; do
 echo Creating ${i%*.flac}.ogg
 gst-launch-0.10 filesrc location="$i" ! decodebin ! audioconvert !  lame bitrate=160 ! filesink location="${i%*.flac}.mp3"
done

They require the usage of gstreamer set of codecs, in Ubuntu gstreamer comes preinstalled but you may need the mp3 codec

sudo apt-get gstreamer0.10-lame 

(note that the version may change...)