Difference between revisions of "Website:WormMine Builds"
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Jump to navigationJump to search (Added stub for WS240 ACeDB dump.) |
(WS240 output of ACeDB dump added.) |
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Line 9: | Line 9: | ||
Path: <code>/home/jbaran/src</code> | Path: <code>/home/jbaran/src</code> | ||
− | Command: <code>./website-intermine/scripts/dump_ace.sh / | + | Command: <code>./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws240</code> |
Output: | Output: | ||
− | < | + | <pre> |
+ | 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> | ||
=== WS239 === | === WS239 === |
Revision as of 20:50, 18 November 2013
WS240
Build
ACeDB Dump
Host: WormMine dev server (206.108.125.174)
Path: /home/jbaran/src
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
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