Re: [galaxy-dev] stdout and stderr while using pbs
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 you need to capture stderr to prevent it from causing a failure, please see this page: https://bitbucket.org/galaxy/galaxy-central/wiki/Job_failure_when_stderr --nate Reagrds shashi shekhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] stdout and stderr while using pbs
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 the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] stdout and stderr
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 mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
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 . 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 mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
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, https://bitbucket.org/galaxy/galaxy-central/issue/325/ Until that is fixed, you'll probably need a wrapper script, there is an example of this in tools/ncbi_blast_plus/hide_stderr.py Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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 of the process where it is and when it's expected to be finished. Indeed a wrapper can be used but if you just have a plain cmdline with options in your tool xml you can use 1dev/null and 2dev/null (or 2- and 1- in short). For the XML to keep it valid you need to encode the and into: 2gt;amp;- Or port both into a logfile which you specify as output. 2$logfile (2gt;$logfile) Alex Van: galaxy-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 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 mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
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! Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: donderdag 26 mei 2011 15:19 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 of the process where it is and when it's expected to be finished. Indeed a wrapper can be used but if you just have a plain cmdline with options in your tool xml you can use 1dev/null and 2dev/null (or 2- and 1- in short). For the XML to keep it valid you need to encode the and into: 2gt;amp;- Or port both into a logfile which you specify as output. 2$logfile (2gt;$logfile) Alex Van: galaxy-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 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 mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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 though when errors occur! Right - if you need to detect an error state via the return code, currently you have to do this with a wrapper script. If you don't ever expect any errors, then you can treat stderr as an output, or just redirect to to /dev/nul - but I don't like that idea - silent failures are bad. I regard fixing issue 325 as one of the top priorities in Galaxy, but in the short term I'd settle for treating any output on stderr OR a non-zero return code as a failure. i.e. Something like this patch, even if more work is needed for PBS jobs: https://bitbucket.org/galaxy/galaxy-central/issue/325/#comment-331776 Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
Peter, can't agree more. Its more a workaround to get warnings not turning up red. Porting it to the log file would mean you have to check the logfile! Alex Van: Peter Cock [p.j.a.c...@googlemail.com] Verzonden: donderdag 26 mei 2011 16:04 Aan: Bossers, 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 though when errors occur! Right - if you need to detect an error state via the return code, currently you have to do this with a wrapper script. If you don't ever expect any errors, then you can treat stderr as an output, or just redirect to to /dev/nul - but I don't like that idea - silent failures are bad. I regard fixing issue 325 as one of the top priorities in Galaxy, but in the short term I'd settle for treating any output on stderr OR a non-zero return code as a failure. i.e. Something like this patch, even if more work is needed for PBS jobs: https://bitbucket.org/galaxy/galaxy-central/issue/325/#comment-331776 Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] stdout and stderr
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
