Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Cole chris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Just realised I hadn't copied the list into the reply.
No there are no errors in the browser (Firefox 4 beta7) and this was working normally in the same browser prior to the update to galaxy-dist.
On 12/11/10 22:33, Kanwei Li wrote:
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
[ copying in the galaxy user mailing list as this is also a problem with the main site ]
OK. I think I've pinned this down to a problem between Firefox 4 beta (both on Linux and OSX) and the latest version of Galaxy-dist.
Prior to updating my local install of Galaxy-dist, Firefox 4 beta worked fine with job tracking, but with the latest update it fails to track properly. This also occurs with a 'clean' install of Galaxy-dist, so it's not some trailing config problem with my set-up.
Firefox 3.6.12 works fine.
Does anyone else see similar behaviour? Cheers,
Chris
On 15/11/10 16:26, Chris Cole wrote:
Just realised I hadn't copied the list into the reply.
No there are no errors in the browser (Firefox 4 beta7) and this was working normally in the same browser prior to the update to galaxy-dist.
On 12/11/10 22:33, Kanwei Li wrote:
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
What revision was your galaxy-dist that worked? The current galaxy-dist is a month old. Does it fail for long jobs or even for simple, fast jobs like uploading a small file?
-Kanwei
On Tue, Nov 16, 2010 at 4:59 AM, Chris Cole chris@compbio.dundee.ac.uk wrote:
[ copying in the galaxy user mailing list as this is also a problem with the main site ]
OK. I think I've pinned this down to a problem between Firefox 4 beta (both on Linux and OSX) and the latest version of Galaxy-dist.
Prior to updating my local install of Galaxy-dist, Firefox 4 beta worked fine with job tracking, but with the latest update it fails to track properly. This also occurs with a 'clean' install of Galaxy-dist, so it's not some trailing config problem with my set-up.
Firefox 3.6.12 works fine.
Does anyone else see similar behaviour? Cheers,
Chris
On 15/11/10 16:26, Chris Cole wrote:
Just realised I hadn't copied the list into the reply.
No there are no errors in the browser (Firefox 4 beta7) and this was working normally in the same browser prior to the update to galaxy-dist.
On 12/11/10 22:33, Kanwei Li wrote:
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
I'm afraid I don't know. I hadn't updated for a several months, though. Is there a way I can find out from mercurial?
It fails for everything in Firefox4 and also history items are unclickable. Do you not see it at http://main.g2.bx.psu.edu/ with Firefox4?
Chris
On 16/11/2010 19:07, Kanwei Li wrote:
What revision was your galaxy-dist that worked? The current galaxy-dist is a month old. Does it fail for long jobs or even for simple, fast jobs like uploading a small file?
-Kanwei
On Tue, Nov 16, 2010 at 4:59 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
[ copying in the galaxy user mailing list as this is also a problem with the main site ]
OK. I think I've pinned this down to a problem between Firefox 4 beta (both on Linux and OSX) and the latest version of Galaxy-dist.
Prior to updating my local install of Galaxy-dist, Firefox 4 beta worked fine with job tracking, but with the latest update it fails to track properly. This also occurs with a 'clean' install of Galaxy-dist, so it's not some trailing config problem with my set-up.
Firefox 3.6.12 works fine.
Does anyone else see similar behaviour? Cheers,
Chris
On 15/11/10 16:26, Chris Cole wrote:
Just realised I hadn't copied the list into the reply.
No there are no errors in the browser (Firefox 4 beta7) and this was working normally in the same browser prior to the update to galaxy-dist.
On 12/11/10 22:33, Kanwei Li wrote:
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Got it, fixed on trunk. Thanks for reporting it!
On Tue, Nov 16, 2010 at 4:00 PM, Chris Cole chris@compbio.dundee.ac.uk wrote:
I'm afraid I don't know. I hadn't updated for a several months, though. Is there a way I can find out from mercurial?
It fails for everything in Firefox4 and also history items are unclickable. Do you not see it at http://main.g2.bx.psu.edu/ with Firefox4?
Chris
On 16/11/2010 19:07, Kanwei Li wrote:
What revision was your galaxy-dist that worked? The current galaxy-dist is a month old. Does it fail for long jobs or even for simple, fast jobs like uploading a small file?
-Kanwei
On Tue, Nov 16, 2010 at 4:59 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
[ copying in the galaxy user mailing list as this is also a problem with the main site ]
OK. I think I've pinned this down to a problem between Firefox 4 beta (both on Linux and OSX) and the latest version of Galaxy-dist.
Prior to updating my local install of Galaxy-dist, Firefox 4 beta worked fine with job tracking, but with the latest update it fails to track properly. This also occurs with a 'clean' install of Galaxy-dist, so it's not some trailing config problem with my set-up.
Firefox 3.6.12 works fine.
Does anyone else see similar behaviour? Cheers,
Chris
On 15/11/10 16:26, Chris Cole wrote:
Just realised I hadn't copied the list into the reply.
No there are no errors in the browser (Firefox 4 beta7) and this was working normally in the same browser prior to the update to galaxy-dist.
On 12/11/10 22:33, Kanwei Li wrote:
Sounds like a browser issue, what browser are you using and are there any errors in the browser?
On Fri, Nov 12, 2010 at 11:11 AM, Chris Colechris@compbio.dundee.ac.uk wrote:
Hi,
Another problem in the update I've applied. New jobs don't change state in the Galaxy interface, but they are being correctly farmed onto our cluster via DRMAA. THis is the output I get:
galaxy.jobs INFO 2010-11-12 16:02:43,029 job 2187 dispatched galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) submitting file /homes/www-galaxy/galaxy_devel/database/pbs/galaxy_2187.sh galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:43,836 (2187) command is: perl /homes/www-galaxy/local_tools_devel/bin/get_RNA_align.pl --rna hsa-mir-30a --num-reads 1 --expt smRNAHelaC --format text --order pos --out /homes/www-galaxy/galaxy_devel/database/files/002/dataset_2317.dat --noverbose galaxy.jobs.runners.drmaa INFO 2010-11-12 16:02:43,857 (2187) queued as 989766 galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:44,820 (2187/989766) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:46,824 (2187/989766) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:48,121 (2187/989766) state change: process status cannot be determined galaxy.jobs.runners.drmaa DEBUG 2010-11-12 16:02:50,128 (2187/989766) state change: job finished normally galaxy.jobs DEBUG 2010-11-12 16:02:50,530 job 2187 ended
If I manually refresh the history panel then the grey history item goes green. Anyone else seen this behaviour? Thanks,
Chris
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Dr Chris Cole Senior Bioinformatics Research Officer College of Life Sciences University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096
galaxy-dev@lists.galaxyproject.org
-
Chris Cole -
Kanwei Li