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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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

Install and run salmon-0.10.0 and Trinity-2.6.6

Owned by Lingsheng Dong
Last updated: May 06, 2021 by Neil Coplan
1 min read

Start an interactive job, with a walltime of 12 hours, 2000MB of memory. Load related modules:

srun --pty -p interactive -t 0-12:0:0 --mem 3G -c 2 /bin/bash

Create a directory in home, download and compile trinity:

mkdir -p ~/pub/trinity cd ~/pub/trinity wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz tar xvzf Trinity-v2.6.6.tar.gz cd trinityrnaseq-Trinity-v2.6.6/ module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 make make plugins

Create a directory in home and download salmon. Note: this a binary, does not need to compile

mkdir -p ~/pub/salmon cd ~/pub/salmon wget https://github.com/COMBINE-lab/salmon/releases/download/v0.10.0/salmon-0.10.0_linux_x86_64.tar.gz tar xvzf salmon-0.10.0_linux_x86_64.tar.gz

Test run Trinity using test data

For downstream analysis, please visit: https://github.com/trinityrnaseq/trinityrnaseq/wiki

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