Website:WormMine Builds

From WormBaseWiki
Jump to: navigation, search

WS244

Build

AceDB Dump

Host: dev.wormbase.org

User: intermine

Path: /home/intermine

Command: ./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws244

Note: DO NOT add a trailing backslash after the path

Output

./website-intermine/scripts/dump_ace.sh /mnt/ephemeral0/acedb_dump_ws244
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
// Session 594 is readlocked by acabunoc since 2014-08-11_18:29:04 using tace (process 31767 on machine dev.wormbase.org)
// Session 594 is readlocked by getLoginFailed since 2014-08-11_19:28:09 using tace (process 672 on machine dev.wormbase.org)
acedb> 
// Found 223435 objects
// 223435 Active Objects
acedb> // 223435 objects dumped
// 223435 Active Objects
acedb> 
// Found 199169 objects
// 199169 Active Objects
acedb> // 199169 objects dumped
// 199169 Active Objects
acedb> 
// Found 201722 objects
// 201722 Active Objects
acedb> // 201722 objects dumped
// 201722 Active Objects
acedb> 
// Found 239936 objects
// 239936 Active Objects
acedb> // 239936 objects dumped
// 239936 Active Objects
acedb> // ERROR -  Failed to open for reading: /home/intermine/website-intermine/acedb-dev/acedb/species.ace (system error 2 - No such file or directory)
// Sorry, I could not open file /home/intermine/website-intermine/acedb-dev/acedb/species.ace
// 239936 Active Objects
acedb> // 239936 objects dumped
// 239936 Active Objects
acedb> // 239936 Active Objects
acedb> 
// A bientot


Pre-Processing

Host: WormMine dev server (206.108.125.174)

User: intermine

Path: /nfs/wormbase/data/acedmp

Commands:

mkdir WS244
cd WS244
scp acabunoc@dev.wormbase.org:/mnt/ephemeral0/acedb_dump_ws244/* .
cd /home/intermine/website-intermine/acedb-dev/intermine/redeployment
# Set "release = WS244" in update.properties
ant

Build failed with error: /nfs/wormbase/data/intermine/redeployment/build.xml:68: Property 'bpid-c_sp11' is not defined.

Fixed by changing c_sp11 to c_tropicalis in genomic-fasta-species.txt, protein-fasta-species.txt and gff3-species.txt



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: WS244
DATABASE NAME: wormmine_ws244
Updating ~/.intermine/wormmine.properties...
Updating project.xml...
Building the InterMine database...

Quick fix for resolving missing organisms.xml file:

cd /nfs/wormbase/data/intermine/datadir
mkdir entrez-organism
cp /home/intermine/organisms.xml entrez-organism


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