Hi Bassam,

I think that your best bet is to explore this command usage in general, since this is really a unix question and no detail about how you used this in Galaxy was provided for others to comment on. I am assuming that you already checked your Galaxy process and found out if it already ran and restarted it or did whatever you needed to do to get your work done.

There isn't much more to add at the basic level so you should certainly go forward - we might get a admin to comment on when or if they use nohup, but this is a fairly common utility, and doing some research on how to use it (beyond the pointers I sent out) is the next move. You will likely find with a quick search both a unix forum where the grinding details are discussed among seasoned admins and a friendly web page where common usage cases are explained in patient detail - plus the full spectrum of advice in-between (some good/some ?).

Please do keep all follow-up on the list and start brand new threads for new questions with just a "to" to the mailing list - not any team members, this greatly helps us to track and provide expedient feedback. If you do have a problem with a specific process - I would start fresh with a new thread (new message, not just a reply with the subject line changed).
http://wiki.galaxyproject.org/Support#Mailing_Lists

For the best chance at a good reply, be specific about exactly what you are doing, if you are on a local or cloud (assuming local from your comments, but this will be a new thread, so include it), what changeset you are running, what sort of troubleshooting you have done already, etc. Those sorts of details help so that advice can be specific to help you solve the problem - vague questions are difficult to address since so many things could be factors. But don't be afraid to ask if you are stuck - give as much detail as you can and send it out - everyone started new at some point!
Here is some help about asking good questions:
http://wiki.galaxyproject.org/MailingLists?action=show&redirect=Mailing+Lists#New_to_Mailing_Lists.3F

Take care,

Jen
Galaxy team

On 2/6/13 4:25 PM, Bassam Tork wrote:> Dear Jennifer,
Thank you so much. Should I wait to receive email from
galaxy-...@bx.psu.edu <mailto:galaxy-...@bx.psu.edu> or could I check
the posting and answers from some web pages?
Thanks.
Bassam Tork.


On 2/6/13 12:13 PM, Jennifer Jackson wrote:
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,

Jen
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
http://galaxyproject.org
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