These instructions are for JGI internal use.

If a taxonomy server or Sketch server dies:

Look at /global/projectb/sandbox/gaag/bbtools/server/start*Server.sh, which includes:

startTaxServer.sh
startRefseqServer.sh
startProteinServer.sh
startNtServer.sh
startSilvaServer.sh

Each file indicates where to run the script.  So, for example, startTaxServer.sh says: #Run this on gpweb25
ssh to the indicated machine, change directory to /global/projectb/sandbox/gaag/bbtools/server/, and run startTaxServer.sh.
It does not matter which user you are logged in as.  But if you run into permission problems, make a copy of the script somewhere else and run it there.

To update taxonomy, go to /global/projectb/sandbox/gaag/bbtools/tax
1) Create a new directory
2) Copy the old shellscripts from "latest"
3) Execute the shellscripts
4) Point the "latest" symlink to the new directory after execution finishes
5) Restart the taxonomy server

For example:
cd /global/projectb/sandbox/gaag/bbtools/tax/
mkdir feb13_2019
cp latest/*.sh feb13_2019
cd feb13_2019
sh fetchOuter.sh 1>fetch.o 2>&1 &
#(wait until it finishes; it will create a file called "finished" when complete)
cd ..
ln -sfn feb13_2019 latest
#(restart the taxonomy server)