Ok, I added
track_jobs_in_database = True

to universe_wsgi.ini and now workflows appear to go to completion.

Another problem I was having was that steps in a workflow would stay gray even 
though examination of the log revealed the steps had completed and produced 
correct output (as verified by directly opening the dat files).  This problem 
also seems to have been fixed by the above.

Mark

From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of mark.r...@syngenta.com
Sent: Monday, January 28, 2013 1:18 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] workflows stop prematurely

Hi All

On my local install of galaxy I'm having  problems executing workflows.  I will 
upload data into a new history and then select to run a saved workflow.  This 
initiates fine but, after the completion of a variable number of steps, the 
workflow just stops after the successful completion of a step.  No errors 
appear in the web interface and all I can see in the paster.log is something 
like


90 HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
127.0.0.1 - - [28/Jan/2013:12:29:07 -0400] "GET /api/histories/82b264d8c3d11790 
HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:08,621 execution finished: 
python 
/home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_trimmer_by_quality.py 
'/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_590.dat' 
'/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat' -f 
'sanger' -s '5'      -t '1' -e '53' -a 'mean' -x '0' -c '>=' -q '20.0'
galaxy.jobs DEBUG 2013-01-28 12:29:08,838 Tool did not define exit code or 
stdio handling; checking stderr for success
galaxy.tools DEBUG 2013-01-28 12:29:09,135 Error opening galaxy.json file: 
[Errno 2] No such file or directory: 
'/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/418/galaxy.json'
galaxy.jobs DEBUG 2013-01-28 12:29:09,439 job 418 ended
galaxy.jobs DEBUG 2013-01-28 12:29:10,041 (420) Working directory for job is: 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420
galaxy.jobs.handler DEBUG 2013-01-28 12:29:10,042 dispatching job 420 to local 
runner
galaxy.jobs.handler INFO 2013-01-28 12:29:10,200 (420) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,385 Local runner: starting 
job 420
galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,759 executing: python 
/home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_filter.py 
/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/tmph0Ll2V
 /home/rosema1/Projects/galaxy-dist/database/files/000/dataset_594.dat 
/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/dataset_594_files
 'sanger'
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET /api/histories/82b264d8c3d11790 
HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET /api/users/f2db41e1fa331b3e 
HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET 
/api/histories/82b264d8c3d11790/contents?ids=3da459a26c8f00b4%2C736af8f0a76a2e71
 HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"

127.0.0.1 - - [28/Jan/2013:12:29:16 -0400] "GET /api/histories/82b264d8c3d11790 
HTTP/1.1" 200 - "http://127.0.0.1:8081/history"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"

Though I seem to see this even when a step completes and the workflow proceeds.

Moreover, if I then begin executing the next steps in the workflow, they work, 
but create new entries in the history.

So, some questions:

Why is this happening and what can I do to get workflows to run to completion?

Also,  is it possible to reinitiate the workflow from the premature stopping 
point without having to launch each step individually and point each at new 
inputs rather than the ones dictated in the workflow?

Thanks

Mark





________________________________
This message may contain confidential information. If you are not the 
designated recipient, please notify the sender immediately, and delete the 
original and any copies. Any use of the message by you is prohibited.



This message may contain confidential information. If you are not the 
designated recipient, please notify the sender immediately, and delete the 
original and any copies. Any use of the message by you is prohibited. 
___________________________________________________________
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/

Reply via email to