The content and subpages given here describe and refer to legacy operations of the Broad GDAC, i.e. essentially TCGA. 

 

GDAC Workspaces and Runs (old planning)

DS TAP (2014) Application Documentation

DS Portal Technology Prototype

Installing/Upgrading Bamboo

Starting Bamboo server

The CentOS gdac1 VM was retired on 2016_10_31, replaced with the Redhat 6.x x86_64 VM vgdac1. For the record, below was the cron table owned by the gdac role account on the gdac1 VM.


SHELL=/bin/tcsh
MAILTO=gsaksena@broadinstitute.org,mnoble@broadinstitute.org,dheiman@broadinstitute.org,timdef@broadinstitute.org

#0 0 * * * ~gdac/bin/choose_dotkit R-2.15 ~gdac/bin/gdac_ingestor --dcc --dccxml --dice /xchip/gdac_data/dcc_mirror3/control/gdacIngestor.cfg && ~gdac/bin/gdac_maf_dashboard
#0 2 * * * ~gdac/bin/gdac_ingestor --jamboree /xchip/gdac_data/dcc_mirror3/control/gdacIngestor.cfg
#0 3 * * * ~gdac/bin/gdac_ingestor --other /xchip/gdac_data/dcc_mirror3/control/gdacIngestor.cfg

MAILTO=mnoble@broadinstitute.org,dheiman@broadinstitute.org,timdef@broadinstitute.org
# */5 * * * * umask 002; nice ~gdac/bin/gdac_run_logger -a ~gdac/bin/gdac_cron monitor

# Several entries have been moved to vgdac1 crontab:
# firebrowse_monitor
# Firehose/fiss analysis_sset_loop (+ stuck job detector)
# firehose_get_scan
# gdac_tester: simply commented out below

# */15 * * * * umask 002; nice ~gdac/bin/gdac_run_logger -a -l ~gdac/logs/gdac_cron_awg ~gdac/bin/gdac_cron awg monitor

# 30 */4 * * * nice ~gdac/bin/gdac_data -R > $HOME/runs/sampleReports/all.html

# */10 * * * * ~gdac/bin/gdac_monitor -m -p $HOME/runs/operations/gdac_monitor_output.html

# 0 6 * * * ~gdac/bin/gdac_jira -c analyses -w -p $HOME/runs/operations/gdac_jira_report -f

# 0 1 * * 6 find /broad/hptmp/gdac/mongo3_fbdev_db -exec touch {} \;

# 0 2 * * 6 find /broad/hptmp/gdac/fh2gdc -exec touch {} \;

# 30 8 * * * ~gdac/bin/gdac_tester /xchip/tcga/Tools/gdac/tester/configs/testGDACPackages.cfg