Hi Bassam,

First, I am going to post your question to the galaxy-...@bx.psu.edu mailing list. This is where local and cloud install Galaxy questions can get the best exposure to the development community.

Next, this isn't necessarily an error. And was the full line really this?

nohup: ignoring input and redirecting stderr to stdout

This is more of a linux issue than a Galaxy issue, but I'll give some feedback and others can comment as well (or a google will bring up many threads on the topic). Basically, this is just a stderr warning and can be ignored. IF you should be using it - nohup isn't for all jobs.

Personally, I use it for data processing sometimes (general use, not part of running Galaxy), but I think I am the only one (here!), since there are other options to keep processes detached from individual sessions. It is a habit. I see this all the time and the job keeps on running. I could redirect the stderr to /dev/null but I usually just ignore it (lazy = type less characters). But I don't admin our Galaxy server either and wouldn't consider using it for that purpose. Which is why I am posting to the mailing list, where the admins can comment.

On your system, the process might have actually run - this message has nothing to do with it running or not. But you want to be careful - if the process is interactive (requires a password), you don't want to use nohup and redirect both stdout and stderr. I don't know what command you ran, but you can do a few things to check to see if the process is running:

See if the nohup.out file is keeping a log of some sort of the job (if it is still running, or if it quit and put output here):

$ more nohup.out

See what jobs are running in the current session:

$ jobs

See what jobs are assigned to the Galaxy user, you can do something like:

$ ps -u galaxy

Check to see if what you asked the process to do has been done, or check the other galaxy logs for activity along those lines.

I am not sure if this is helpful or not, but perhaps will point you in the correct direction (linux command help/usage) where you can find out more.

Take care,

Galaxy team

On 2/6/13 11:24 AM, Bassam Tork wrote:
  Dear Jennifer,
When I ran galaxy on our server it gave the error:

nohup: ignoring input

although I provided all inputs
Appreciate your help.
Bassam Tork.

Jennifer Hillman-Jackson
Galaxy Support and Training
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