Difference between revisions of "Website:WormMine Builds"
(Changed ACeDB dump instructions for user "intermine".) |
(Added information about InterMine WS240 build.) |
||
Line 100: | Line 100: | ||
Output: ''too long to show here'' | Output: ''too long to show here'' | ||
+ | |||
+ | ===== InterMine Build ===== | ||
+ | |||
+ | Host: WormMine dev server (206.108.125.174) | ||
+ | |||
+ | User: intermine | ||
+ | |||
+ | Path: <code>/home/intermine/website-intermine</code> | ||
+ | |||
+ | Command: <code>./scripts/build_intermine.sh WS240</code> | ||
+ | |||
+ | Output (stdout, stderr not shown): | ||
+ | |||
+ | <pre> | ||
+ | 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 | ||
+ | </pre> | ||
=== WS239 === | === WS239 === |
Revision as of 16:01, 29 January 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
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