Software and Utilities

From GO Wiki
Jump to navigation Jump to search

The purpose of the Software and Utilities group (SWUG) is to support both the GOC and the user community with technical, software, bioinformatics and computer-science related matters. In addition, this group will help drive the GOC through the research and provision of new computational technologies and methodologies relating to ontologies and ontology-based data analysis. This group is responsible for creating, clarifying and extending the common model that underpins all of GO. Ontology development tools are necessary for the Ontology Development group to perform its function. In addition, the Annotation Outreach group and wider community need means of exploring and utilizing GO and existing annotations. This group complements all the other groups.

Software and Utilities group summary

Meetings

See Category:SWUG-TCons for all new meetings

  • Visualisation meeting, 2007-08-16. No notes, demo only
  • March 14 2007 -

Past Meetings:

Forthcoming meetings:

Schedule to be decided

Reports

Mail List

There is no public mailing list for this group.

Resources

Documentation

Trackers

People

Principles

Wiki

All software-and-utilities pages on the wiki should go in the wikispace SWUG (SoftWare Utilities Group)

Projects

Galaxy

Everything you need to know about GO Galaxy

OBO-Edit

AmiGO

General Interest

Internal interest

RefGenome

TreeCurationTool

Collaboration with PantherDB


GO database and go-perl

Main page: http://www.geneontology.org/GO.database.shtml

  • gp2protein report This is a script run "peridically" to cross-check gp2protein files submitted by mods.

GO production server cron jobs

  • GO Production Servers AmiGO2
For AmiGO 2:  loading server = golr, user = golr
*Daily GOlr update
 5 0 * * * /tools/admin/scripts/load-golr

For AmiGO 2:  web server = amigo2a & amigo2b, user = golr
* no cronjobs
  • GO Production Servers AmiGO1
For AmiGO 1: (golite & goterm)  loading server = claret, user = mysql
*Perform GO loads
5 0 * * * /db0/home/mysql/bin/load-go-data-wrapper goterm > /dev/null 2>&1
30 1 * * 6 /db0/home/mysql/bin/load-go-data-wrapper-bulk golite > /dev/null 2>&1

*Download uniprot files for GO loading when a new release is available
5 12 * * 6 /db0/home/mysql/bin/get_uniprot_files.pl

*Perform mysqldump
35 11 * * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl goterm go
5 01 * * 1 /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl golite go

*Copy GO loads into ftp area
*bumped 10 hours forward as dumpowl is sloooow
* needs manual manipulation depending on how long the load takes.
00 12 * * * /db0/home/mysql/bin/copy-go-to-ftp term
35 01 * * 2 /db0/home/mysql/bin/copy-go-to-ftp lite
For AmiGO 1: (gofull)  loading server = oro-new, user = mysql
* Perform GO load
45 1 1 * * /db0/home/mysql/bin/load-go-data-wrapper-bulk gofull > /dev/null 2>&1

*Copy GO loads into ftp area
(has to be manually run after gofull run finishes)
#45 1 7 * * /db0/home/mysql/bin/copy-go-to-ftp full
40 06 08 07 * /db0/home/mysql/bin/copy-go-to-ftp full

*Perform mysqldump
45 1 20 * * /db0/home/mysql/bin/mysqlDumpBackupLinuxCompress.pl gofull go

For AmiGO 1: web server = goweb1, user = mysql

*Kill runaway MySQL GO queries
0-59/5  * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl

*Monitor load and if high print all running processes
0-59/12 * * * * /db0/home/mysql/bin/monitor-load.pl

*Refesh cache after golite load
00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl

*clean up cache and sessions
1 * * *  * /share/goweb/www-data/bin/refresh-wrapper.sh
For AmiGO 1: web server = goweb2, user = mysql

*Kill runaway MySQL GO queries
0,5,10,15,20,25,30,35,40,45,50,55 * * * * /db0/home/mysql/bin/kill-wild-mysqld.pl

* Monitor load and if high print all running processes
0-59/5 * * * * /db0/home/mysql/bin/monitor-load.pl

*Refesh cache after golite load
00 12 * * 1 /share/goweb/www-data/html/go-dev/amigo/refresh.pl

*clean up cache and sessions
1 * * *  * /share/goweb/www-data/bin/refresh-wrapper.sh
  • GO scripts by Mike (from Stuart’s email)
For GAF processing scripts server=meatloaf user=gocvs

*GO Processing
20 3 1 * * /share/go/bin/monthly-save.script

*for GO home page
*process gene-association files and output included HTML files
0 2,6,12,14,18,23 * * * /share/go/bin/namespace-counts.pl

*copy repository to ftp space
10,40 * * * * /share/go/bin/copy_repository.go >> /share/go/logs/copy_repository.go.log 2>&1

*Gene Association Filtering Script
45 19 * * * /share/go/bin/filter-gene-association-wrapper.pl

*Counts for Annotation Table
45 21 * * * /share/go/bin/GO-HTML-counts.pl

*added per Cherry GOCVS sandbox
10 2 * * * /share/ftp/go/software/utilities/sf-ontology-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1
20 2 * * * /share/ftp/go/software/utilities/sf-annotation-tracker-digest.pl >> /share/go/logs/sourceforce-trackers.log 2>&1

  • There are other jobs run as root, but those are mostly things like backups and fixing file ownerships at the filesystem level.

SO

Main page: http://www.sequenceontology.org

MiSO

CVS http://song.cvs.sourceforge.net/song/software/scripts/miSO

browser http://song.sf.net/SO_view/index.html

Cross-products in SO

SO contains cross-product definitions of many composite terms. See SO Cross Products for the methodology.

Obol

http://www.berkeleybop.org/obol

Reference Genome Software Prototype

Sohel Merchant has created a prototype as support for the Reference Genome Annotation Project. Currently the project data is managed by means of a google spreadsheet that is difficult to use. The new database and interface will allow the administrator to enter new target genes and for the model organism curators to call their orthologs and to track curation progress of each gene. (For more on the Reference Genome Annotation Project: http://gocwiki.geneontology.org/index.php/Reference_Genome_Annotation_Project )

To access the prototype: http://rails-dev.bioinformatics.northwestern.edu:24000