Restarting BBTools Servers
Instructions for JGI internal use on restarting BBTools taxonomy and sketch servers, and updating taxonomy data.
These instructions are for JGI internal use.
Server Failure Recovery
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 the appropriate start script.
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.
Updating Taxonomy
To update taxonomy, go to /global/projectb/sandbox/gaag/bbtools/tax
- Create a new directory
- Copy the old shellscripts from "latest"
- Execute the shellscripts
- Point the "latest" symlink to the new directory after execution finishes
- Restart the taxonomy server
Example Process
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)Support
For questions and support:
- Email: bbushnell@lbl.gov
- Documentation: bbmap.org