From: Srinivas Maddhi <>
Reply-To: Discussion among end-users of Galaxy <GALAXY-USERS@LIST.UIOWA.EDU>
Date: Tuesday, October 9, 2012 3:40 PM
Subject: [GALAXY-USERS] Helium maintenance: 7:00 AM Mon, 10/15 to 7:00 AM Tue, 10/16

Hello Galaxy users,

The Helium cluster will be undergoing maintenance from 7:00 AM on Monday, 10/15/2012 through 7:00 AM on Tuesday 10/16/2012. While the Galaxy web site itself will remain available during this maintenance window, any existing jobs running on the cluster will be terminated at the start of the maintenance window and new jobs will not be able to be initiated during the maintenance window. Sorry about the lack of additional advance notice of this maintenance.

We will send an email to this mailing list once Helium is back up and available.

Please let us know if you have any questions by replying to the sender of this email (

Thank you.

IIHG Galaxy Administration Team

Galaxy @ Iowa brought to you by:
Iowa Institute for Human Genetics
Center for Bioinformatics and Computational Biology
Iowa High Performance Compute Cluster

IIHG = Iowa Institute for Human Genetics. Haven't heard of it? Don't worry - it is very new! You can read more about it via the Gazette article here : or visit the IIHG Website:

IIHG sponsored a bioinformatics short course August 3-6th, 2012, at the University of Iowa. Over 50 participants listened about Next Generation Sequencing concepts and the magic of Massively Parallele Sequencing (MPS) from both local and guest speakers. The course also included 3 in-depth hands on labs all using the Galaxy platform.

Missed it? No need to fret! All lectures were recorded and can be playedback at any time: IIHG Bioinformatics Course

Galaxy has now moved onto its permanent home! It can now be accessed at With this move, we now have the following improvements:

  • Large sftp space! We are no longer limited to a ~350 GB sftp space. files uploaded will reside on Helium's scratch space until they are imported into Galaxy
  • Moved jobs to the all.q (you can read about Helium queue's here: Link to Helium Queue Usage Info 
    ). This means we are no longer capped at 25 jobs. If a job is killed to make room for investors, it is automatically re-dispatched to a new compute node for you.
  • Official server certificates. You should no longer see security warnings when accessing Galaxy.
  • Dedicated Galaxy box with all the fixins.

All your data and histories should still be in tact. Don't hesitate to post to the galaxy-users listserv if you experience any unexpected problems, it could be related to the move.


The move of Galaxy to its new production server has been postponed. There will not be a Galaxy outage this Thursday as originally planned.

I do not have a firm date for when Galaxy will move to its new server, but it will be sometime before Friday, May 11th.


The time has come to move off of our Helium test server ( and onto Galaxy's permanent Helium home ( The target is to have helium fully moved by Friday, April 27, 2012. This should not impact any in-flight work so long as it is completed by Thursday evening. Starting Thursday I will block the ability for anyone to submit new jobs via galaxy, kill off any outstanding Galaxy jobs, and migrate the database. An email will be posted to galaxy-users when the migration is completed and Galaxy is re-open for business.


All you RNA Seq people, the Tuxedo suite of tools is now exposed in Galaxy. I am not claiming it is error free, but ready to test. Right now only hg19, hg18 and e_coli indices are installed and wired into Galaxy for the tool's use. More reference indices can be exposed upon request.

Here are the tool versions I installed.

Bowtie: 0.12.7
TopHat: 1.3.2
Cufflinks: 1.3.0

I have done basic sniff testing which passes. Enjoy!

So after all my claims of campus only & UIAnywhere access to Galaxy on Helium (did you like my warning boxes??) I was called on it ... and it failed. Doh. I vpn to campus through CBCB's custom vpn configuration and it always worked for me and assumed that UIAnywhere would as well. Ever heard the saying about ASSUME... ASS/U/ME? Turns out when vpning over UIAnywhere, you can get to other campus address spaces I did not know existed. Good thing the Helium experts respond so quickly (and on a weekend).

Now i have all the firewall rules in place and my UIAnywhere tests allow me access to Galaxy. whew. Also at the same time I received the address space for UIHC and so now Galaxy should be accessible from UIHC - awaiting confirmation on this one though.