[galaxy-dev] The job is finished..but not in the history
hi,
I'm writing some wrappers to connect galaxy with some
scripts/programs. I can't understand why, for some, the job in the
history never end.
Here an example of the log output
<output>
127.0.0.1 - - [20/Aug/2010:14:18:38 +0200] "GET /history HTTP/1.1" 200
- "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (X11; U;
Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6
(Debian-3.0.6-3)"
galaxy.jobs DEBUG 2010-08-20 14:18:41,524 job 81 dispatched
galaxy.jobs.runners.local DEBUG 2010-08-20 14:18:41,694 executing:
python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir
/home/extuser/raffo/chromosomes/hg19 --im
/home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out
/home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20
127.0.0.1 - - [20/Aug/2010:14:18:42 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64;
en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
127.0.0.1 - - [20/Aug/2010:14:18:46 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64;
en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
...
...
...
127.0.0.1 - - [20/Aug/2010:14:19:18 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64;
en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
galaxy.jobs.runners.local DEBUG 2010-08-20 14:19:20,831 execution
finished: python
/home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir
/home/extuser/raffo/chromosomes/hg19 --im
/home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out
/home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20
127.0.0.1 - - [20/Aug/2010:14:19:22 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64;
en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
127.0.0.1 - - [20/Aug/2010:14:19:27 +0200] "POST
/root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64;
en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)"
...
...
...
and so on
</output>
If i check the "running" dataset clicking the eye i see the final
result that I expect....
Then, checking in the table 'dataset' (in universe.sqlite) i obtain
87|running
why the flag isn't changed to ok?
any ideas?
Tnx :)
raf