jpayne@68: These instructions are for JGI internal use.
jpayne@68: 
jpayne@68: If a taxonomy server or Sketch server dies:
jpayne@68: 
jpayne@68: Look at /global/projectb/sandbox/gaag/bbtools/server/start*Server.sh, which includes:
jpayne@68: 
jpayne@68: startTaxServer.sh
jpayne@68: startRefseqServer.sh
jpayne@68: startProteinServer.sh
jpayne@68: startNtServer.sh
jpayne@68: startSilvaServer.sh
jpayne@68: 
jpayne@68: Each file indicates where to run the script.  So, for example, startTaxServer.sh says: #Run this on gpweb25
jpayne@68: ssh to the indicated machine, change directory to /global/projectb/sandbox/gaag/bbtools/server/, and run startTaxServer.sh.
jpayne@68: 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.
jpayne@68: 
jpayne@68: To update taxonomy, go to /global/projectb/sandbox/gaag/bbtools/tax
jpayne@68: 1) Create a new directory
jpayne@68: 2) Copy the old shellscripts from "latest"
jpayne@68: 3) Execute the shellscripts
jpayne@68: 4) Point the "latest" symlink to the new directory after execution finishes
jpayne@68: 5) Restart the taxonomy server
jpayne@68: 
jpayne@68: For example:
jpayne@68: cd /global/projectb/sandbox/gaag/bbtools/tax/
jpayne@68: mkdir feb13_2019
jpayne@68: cp latest/*.sh feb13_2019
jpayne@68: cd feb13_2019
jpayne@68: sh fetchOuter.sh 1>fetch.o 2>&1 &
jpayne@68: #(wait until it finishes; it will create a file called "finished" when complete)
jpayne@68: cd ..
jpayne@68: ln -sfn feb13_2019 latest
jpayne@68: #(restart the taxonomy server)