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I have a Dropbox account for work and one for personal. Is it possible to run both at the same time, storing Dropbox contents in different folders? (i.e. Dropbox/Work and Dropbox/Personal, respectively)

I'm running Ubuntu 12.04. I know that it's possible to run Dropbox from the command-line, but can multiple agents be run at once?

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Yes, this should be possible. Here is a snippet from the gentoo dropbox init script:

 start() {
     ebegin "Starting dropbox..."
     for dbuser in ${DROPBOX_USERS}; do
         start-stop-daemon -b -o -N ${NICENESS} -c $dbuser -S -v -e HOME="/home/$dbuser" -x /home/$dbuser/.dropbox-dist/dropboxd
     done
     eend $?
 }

In your case the commands you need to run would be

HOME="/home/user/.dropbox/work" /home/user/.dropbox-dist/dropboxd
HOME="/home/user/.dropbox/personal" /home/user/.dropbox-dist/dropboxd

be sure to link the ~/.dropbox/work/Dropbox folder created on the first run of each process to ~/Dropbox/Work or ~/Dropbox/Personal or change it using the script described in the dropboxwiki.

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    Do note that running a program with a different $HOME has interesting side-effects (ie: when you click "Open Dropbox Website," the new browser instance also uses the new $HOME). – Naftuli Kay Mar 28 '14 at 18:34

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