Why would you need to run ./autogen.sh that is not a multichain installation command.
This is how you install multichain on linux:
Installing MultiChain – Linux
su (enter root password)
cd /tmp
wget https://www.multichain.com/download/multichain-1.0.1.tar.gz
tar -xvzf multichain-1.0.1.tar.gz
cd multichain-1.0.1
mv multichaind multichain-cli multichain-util /usr/local/bin (to make easily accessible on the command line)
exit
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Please be more specific for further help. Thanks