Hi Zain,

This is in also in reply to your email this morning:
5:54 AM (US Pacific Coast Time)
[galaxy-dev] Same Problems with Galaxy-Project since 3/14/2013 update

For any jobs that may have been terminated, please re-run. As the servers/clusters were brought back up online following the hardware move last week, it is known that a few jobs failed (some through mid-day yesterday).

Also please see below:

On 3/17/13 7:05 PM, Zain A Alvi wrote:
Dear Sir or Madam,

I hope this reaches you well. I am a graduate student at Seton Hall University and it has been a wonderful experience using Galaxy Project's main server (https://main.g2.bx.psu.edu/) for the past few months. Unfortunately, I am experiencing trouble since the update to the servers on Thursday 3/14/2013.  I am facing the following problems:

1) Only the http addresses only work for uploading any file from NCBI. In the past, I could use the NCBI FTP addresses to upload the file without any trouble.
Is this still an issue? Have you re-tested today? If still a problem now, could you provide an example URL so we can test/try to reproduce?

2) Unfortunately, none of the online tools seem to run. All of my tasks state that they are "waiting to run." This message has been there since yesterday.   The tools that I used since the update are cufflinks and cuffdiff.  These tools were working before the update.
The job queue is busy - so a wait is expected for certain job types (RNA-seq jobs fall into this category). The best strategy when using the public Main Galaxy server is to leave waiting jobs alone until they run. Do not stop/restart jobs - you want to preserve their place in the queue.

Since everyone had their jobs re-started at the same time, the wait may be a bit longer than usual, but this is expected to clear as the bulk of jobs process and things normalize again.

If you work is very urgent, the cloud option is always an alternative:
http://usegalaxy.org/cloud

Migrating to the new server home was a big task, and did cause a bit of a backup in job processing, but we feel it was well worth the effort in the big picture. Thank you for your patience while we get everything in order - and for the feedback about any issues that may exist (such as the FTP one above) so that we can address them,

Best,

Jen
Galaxy team

I was wondering, if you could kindly look into this. I would really appreciate it.

Sincerely,

Zain Alvi

---
PhD Student in Molecular BioSciences
Seton Hall University
email: zain.alvi@student.shu.edu
Ph: (973) 710-7149



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