Difference between revisions of "Website:WormMine Builds"
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Revision as of 15:12, 19 June 2014
Contents
WS240
Build
ACeDB Dump
Host: Website dev server
User: intermine
Path: /home/intermine
Command: ./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws240
Output:
Did not specify AceDB dir in $ACEDB. Searching for tace... ACEDB set to: /usr/local/wormbase/acedb/wormbase Transcript ... done. Variation ... done. Phenotype ... done. Expr_pattern ... done. Expression_cluster ... done. Anatomy_term ... done. Expr_cluster ... done. Life_stage ... done. RNAi ... done. **** Program tace, compiled on: May 14 2010 09:21:02 **** **** Using ACEDB 4.9.52, compiled on: May 14 2010 09:20:07 **** Code by: Jean Thierry-Mieg (CNRS, France) mieg@crbm.cnrs-mop.fr Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk Ed Griffiths (Sanger Centre, UK) edgrif@sanger.ac.uk You may redistribute this program and database subject to the conditions in the accompanying copyright file. Anyone interested in maintaining an up-to-date version should contact one of the authors at the above email addresses. // Database directory: /usr/local/wormbase/acedb/wormbase acedb> // Found 204526 objects // 204526 Active Objects acedb> // 204526 objects dumped // 204526 Active Objects acedb> // Found 186343 objects // 186343 Active Objects acedb> // 186343 objects dumped // 186343 Active Objects acedb> // Found 188862 objects // 188862 Active Objects acedb> // 188862 objects dumped // 188862 Active Objects acedb> // Found 221196 objects // 221196 Active Objects acedb> // 221196 objects dumped // 221196 Active Objects acedb> // ERROR - Failed to open for reading: /home/jbaran/src/website-intermine/acedb-dev/acedb/species.ace (system error 2 - No such file or directory) // Sorry, I could not open file /home/jbaran/src/website-intermine/acedb-dev/acedb/species.ace // 221196 Active Objects acedb> // 221196 objects dumped // 221196 Active Objects acedb> // 221196 Active Objects acedb> // A bientot
Pre-Processing
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /nfs/wormbase/data/acedmp
Commands:
mkdir WS240 cd WS240 scp jbaran@dev.wormbase.org:/mnt/ephemeral0/acedb_dump_ws240/* . cd /home/intermine/website-intermine/acedb-dev/intermine/redeployment # Set "release = WS240" in update.properties ant
Output: too long to show here
InterMine Build
Host: WormMine dev server (206.108.125.174)
User: intermine
Path: /home/intermine/website-intermine
Command: ./scripts/build_intermine.sh WS240
Output (stdout, stderr not shown):
USING RELEASE: WS240 DATABASE NAME: wormmine_ws240 Updating ~/.intermine/wormmine.properties... Updating project.xml... Building the InterMine database... action name time in seconds ------------------------------------------------------------- entrez-organism 130 create-chromosome-locations-and-lengths 1075 do-sources 51 create-search-index 3747 summarise-objectstore 740 create-autocomplete-index 41 create-attribute-indexes 191 transfer-sequences 209663 final-dump 1246 total 216884
Quick fix for resolving missing organisms.xml file:
cd /nfs/wormbase/data/intermine/datadir mkdir entrez-organism cp /home/intermine/organisms.xml entrez-organism
Deployment
TBD
WS239
Build
Host: WormMine dev server (206.108.125.174)
Path: /home/jbaran/src/website-intermine/acedb-dev/intermine/wormmine
Command: ../bio/scripts/project_build -l -v localhost joachim_ws239_2
Summary:
action name time in seconds ------------------------------------------------------------- entrez-organism 95 create-chromosome-locations-and-lengths 708 do-sources 25 create-search-index 983 summarise-objectstore 245 create-autocomplete-index 28 create-attribute-indexes 95 transfer-sequences 248429 final-dump 697 total 251305
Deployment
Host: WormMine production server (206.108.125.166)
Path: /nfs/wormbase/archive/jbaran/WS239-2
Commands:
dropdb -U intermine joachim-ws239-2 createdb -U intermine -E SQL_ASCII joachim-ws239-2 pg_restore -U intermine_admin -d joachim-ws239-2 joachim_ws239_2.final
Required Disk Space:
1.3G joachim_ws239_2.final + 17G PostgreSQL DB
Architecture (Web Dev)
Architecture category deals with Installations, Setting up and Configuring systems (particularly the more complex and less common ones).
For routine tasks, refer to category: Maintenance (Web Dev). <categorytree mode=pages>Architecture (Web Dev)</categorytree>