Re: [galaxy-dev] stdout and stderr while using pbs

2011-05-31 Thread Nate Coraor
shashi shekhar wrote: Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Hi Shashi, There's no difference when running via PBS or locally in this regard. If

[galaxy-dev] stdout and stderr while using pbs

2011-05-27 Thread shashi shekhar
Hi All, if i am using pbs . in this i am getting stderror and stdout . then how can i handle such type of problem. can i check the standard error before displaying anything on browser. Reagrds shashi shekhar ___ Please keep all replies on

[galaxy-dev] stdout and stderr

2011-05-26 Thread shashi shekhar
Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Glen Beane
You need a wrapper to capture the stderr It would be nice if there were an option to base a tools status on the unix return value (for well behaved programs) On May 26, 2011, at 8:36 AM, shashi shekhar meshash...@gmail.com wrote: Hi all, I am using one tool which gives stdout and stderr

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Peter Cock
On Thu, May 26, 2011 at 1:36 PM, shashi shekhar meshash...@gmail.com wrote: Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job failed) in browser.How can i resolve such type of problem. Regards shashi shekhar See issue 325,

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens shashi shekhar Verzonden: donderdag 26 mei 2011 14:36 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] stdout and stderr Hi all, I am using one tool which gives stdout and stderr . it is showing red color (job

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
:19 Aan: 'shashi shekhar' CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] stdout and stderr Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as additional output to the tool. I do many times the same since it allows the realtime tracking in the log file

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Peter Cock
On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote: PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won’t get a red box though when errors occur! Right - if you need to detect an error state via the return code,

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
, Alex CC: shashi shekhar; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] stdout and stderr On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote: PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won’t get a red box

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Florent Angly
On 27/05/11 00:04, Peter Cock wrote: I regard fixing issue 325 as one of the top priorities in Galaxy Can't agree more with you Peter! This bug and other tool wrapper related bugs make it harder and more tedious to contribute tool wrappers. It's a big turn off for me. Florent