Using jgit with socks5 proxy on Ubuntu

I use jgit to store my git repositories on Amazon S3. On my laptop I also periodically connect to the internet through tetherbot, which uses a socks proxy (see earlier post for more details there). I finally figured out how to get jgit, and I suppose other java applications working with the proxy. Jgit is java based and you need to pass the right flags to java, as described at http://java.sun.com/javase/6/docs/technotes/guides/net/proxies.html. The flags are:-DsocksProxyHost=localhost -DsocksProxyPort=1080. I inserted the following code into the jgit program, before the exec .... $java_args part:

if (netstat -pl --numeric-ports 2>&1 | grep ':1080.*adb' > /dev/null); then
    echo "Using Java socks5 proxy args"
    java_args="$java_args -DsocksProxyHost=localhost -DsocksProxyPort=1080"
fi

I inserted the lines using emacs. For some reason, xemacs and nano garbled the file when I tried editing it with them.