NOTICE: FULL O2 Cluster Outage, January 3 - January 10th
O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10
- on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
- on Jan 3 (6:00 PM): O2 systems will start being powered off.
This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.
Specifically:
- The O2 Cluster will be completely offline, including O2 Portal.
- All data on O2 will be inaccessible.
- Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
- Websites on O2 will be completely offline, including all web content.
More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation
sratoolkit/2.10.7 to download dbGAP data
- Lingsheng Dong
- Neil Coplan
Owned by Lingsheng Dong
Due to Aspera license limitations, users have to install the software under their home to user the software.Â
Start interactive job, and create working folder and load sratoolkit modue
For example, for user abc123, the working directory will be
srun --pty -p interactive -t 0-12:0:0 --mem 2000MB -n 1 /bin/bash
mkdir /n/scratch/users/${USER:0:1}/${USER}/testDbGaP
cd /n/scratch/users/${USER:0:1}/${USER}/testDbGaP
module load sratoolkit/2.10.7Configure sratoolkit. Only need to do this once:
# Configure sratoolkit
vdb-config --interactive
# Directly press x key to quit
# By default, sratoolkit uses working diretory as cache. It is better to use scratch instead:
echo /repository/user/main/public/root = \"/n/scratch/users/${USER:0:1}/${USER}/ncbi\" >> ~/.ncbi/user-settings.mkfg
Downoading dbGaP repository Key and upload to O2:
# Upload the dbGaP repository Key to O2:
scp ~/Download/prj_phs710EA_test.ngc $USER@transfer.rc.hms.harvard.edu:~/.ncbi