Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/docs/RestartingServers.txt @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@68 | 1 These instructions are for JGI internal use. |
| jpayne@68 | 2 |
| jpayne@68 | 3 If a taxonomy server or Sketch server dies: |
| jpayne@68 | 4 |
| jpayne@68 | 5 Look at /global/projectb/sandbox/gaag/bbtools/server/start*Server.sh, which includes: |
| jpayne@68 | 6 |
| jpayne@68 | 7 startTaxServer.sh |
| jpayne@68 | 8 startRefseqServer.sh |
| jpayne@68 | 9 startProteinServer.sh |
| jpayne@68 | 10 startNtServer.sh |
| jpayne@68 | 11 startSilvaServer.sh |
| jpayne@68 | 12 |
| jpayne@68 | 13 Each file indicates where to run the script. So, for example, startTaxServer.sh says: #Run this on gpweb25 |
| jpayne@68 | 14 ssh to the indicated machine, change directory to /global/projectb/sandbox/gaag/bbtools/server/, and run startTaxServer.sh. |
| jpayne@68 | 15 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 | 16 |
| jpayne@68 | 17 To update taxonomy, go to /global/projectb/sandbox/gaag/bbtools/tax |
| jpayne@68 | 18 1) Create a new directory |
| jpayne@68 | 19 2) Copy the old shellscripts from "latest" |
| jpayne@68 | 20 3) Execute the shellscripts |
| jpayne@68 | 21 4) Point the "latest" symlink to the new directory after execution finishes |
| jpayne@68 | 22 5) Restart the taxonomy server |
| jpayne@68 | 23 |
| jpayne@68 | 24 For example: |
| jpayne@68 | 25 cd /global/projectb/sandbox/gaag/bbtools/tax/ |
| jpayne@68 | 26 mkdir feb13_2019 |
| jpayne@68 | 27 cp latest/*.sh feb13_2019 |
| jpayne@68 | 28 cd feb13_2019 |
| jpayne@68 | 29 sh fetchOuter.sh 1>fetch.o 2>&1 & |
| jpayne@68 | 30 #(wait until it finishes; it will create a file called "finished" when complete) |
| jpayne@68 | 31 cd .. |
| jpayne@68 | 32 ln -sfn feb13_2019 latest |
| jpayne@68 | 33 #(restart the taxonomy server) |