In case anyone is interested, it's a bit complicated, but not impossible.:

First you need to make sure you have a valid and working node setup including node, npm, and node-gyp. This was by far the most complicated part.  Once that was done, the rest was pretty smooth.

Run steamcmd 

force_install_dir /home/steam/screeps
login username
app_update 464350 -beta Server -betapassword the-password-here validate
exit

edit the .screepsrc file in the server directory you just installed:

cd /home/steam/screeps/server/
nano .screepsrc

Next you need to install greenworks. The copy that comes packaged with the server probably won't work for one or more of many reasons. 

git clone https://github.com/greenheartgames/greenworks.git
cd greenworks/
cd deps/
unzip ~/steamworks_sdk_137.zip # you have to get this from your steam developer account
mv sdk steamworks_sdk
cd ..

npm install
cp build/Release/greenworks-linux64.node ~/screeps/server/modules/backend/greenworks/lib/greenworks-linux64.node

Now this will give you a server that still won't run so it's time to rebuild things., then start the server. I combined these into a single script  for starting the server.

#!/bin/bash
cd /home/steam/steamcmd/
./steamcmd.sh +force_install_dir /home/steam/screeps +login user +app_update 464350 -beta Server -betapassword the-password-here validate +exit
cd /home/steam/screeps/server
cp /home/steam/greenworks/build/Release/greenworks-linux64.node ~/screeps/server/modules/backend/greenworks/lib/greenworks-linux64.node
for M in modules/*/
do
pushd $M
rm node_modules -Rf
npm install
npm build
popd
done
pushd modules/driver/native/
node-gyp configure
node-gyp build
popd
rm logs/* -Rf
node modules/launcher/bin/screeps.js start

The script effectively has to download the server every time because of the rebulid, The rebuild it because it just downloaded it. The process doesn't take too long though and it ensures a running, updated, server every time.

Even if screeps was on npm I would probably still do it this way as it most closely matches my other steam game server setups.

But just in case your trying to setup a server, this is what I did, and I hope it helps.

$ uname -a
Linux G5070 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1+deb8u1 (2016-09-03) x86_64 GNU/Linux

greenwork can't `npm install` work with neither of

gyp ERR! node -v v6.9.1
gyp ERR! node-gyp -v v3.4.0

nor

gyp ERR! node -v v0.10.29
gyp ERR! node-gyp -v v0.12.2

# Remove everything related to node, so that `node`, `nodejs`, `npm`, `n` or `node-gyp` is not found.
# Probably not the simplest way but it works.
curl -sL https://deb.nodesource.com/setup_6.x | sudo -E bash - sudo aptitude install -y nodejs
sudo npm install npm@latest -g
sudo npm install node-gyp@latest -g

node -v # v6.9.1
npm -v # 3.10.9
node-gyp -v # v3.4

git clone https://github.com/greenheartgames/greenworks.git
cd greenworks/deps/
unzip ~/path-to/steamworks_sdk_137.zip # It has to be v1.37 and you have to get this from your steam developer account
mv sdk steamworks_sdk
cd ..
npm install