How to get cleanup script to run in cron job ?
Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line: python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i pysqlite>=2 egg successfully loaded for sqlite dialect ########################################## # 2014-11-19 22:07:32 - Handling stuff older than 30 days # Displaying info only ( --info_only ) Deleted 0 histories Elapsed time: 0.0684289932251 ########################################## but if I try to do this in a cron job as follows: 55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1 python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py': [Errno 2] No such file or directory or if I try to do this : 00 22 * * * python /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1 Traceback (most recent call last): File "/media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> from galaxy import eggs ImportError: No module named galaxy Note that I am directing the output to a file only to try to find out why it's not working. Is this a problem with environment? Any suggestions what to try would be much appreciated. Regards James J P Mullan
Hi, Try this : 55 21 * * * cd /media/Store/galaxy/galaxy-dist/ && python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1 I thought you need to be in the galaxy-dist folder when launching the commands. Best, Geert On 11/19/2014 11:14 PM, James Mullan wrote:
Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line:
python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i pysqlite>=2 egg successfully loaded for sqlite dialect ##########################################
# 2014-11-19 22:07:32 - Handling stuff older than 30 days # Displaying info only ( --info_only )
Deleted 0 histories Elapsed time: 0.0684289932251 ##########################################
but if I try to do this in a cron job as follows:
55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py': [Errno 2] No such file or directory
or if I try to do this :
00 22 * * * python /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
Traceback (most recent call last): File "/media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> from galaxy import eggs ImportError: No module named galaxy
Note that I am directing the output to a file only to try to find out why it's not working.
Is this a problem with environment?
Any suggestions what to try would be much appreciated.
Regards James
J P Mullan
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-- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer
Hi Geert, I only saw your reply just now when I checked the archive. I can confirm that I arrived at the same solution myself via http://stackoverflow.com/questions/3287038/cron-and-virtualenv but Thankyou for posting your reply. stackoverflow is a great resource as well as this one. Many Thanks! Regards jamesp Regards Paddy J P Mullan On 19 November 2014 at 22:14, James Mullan <jamespamullan@gmail.com> wrote:
Hello, I am trying to figure out how to run the cleanup scripts in a cron job. The below works on command line:
python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i pysqlite>=2 egg successfully loaded for sqlite dialect ##########################################
# 2014-11-19 22:07:32 - Handling stuff older than 30 days # Displaying info only ( --info_only )
Deleted 0 histories Elapsed time: 0.0684289932251 ##########################################
but if I try to do this in a cron job as follows:
55 21 * * * python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
python: can't open file 'scripts/cleanup_datasets/cleanup_datasets.py': [Errno 2] No such file or directory
or if I try to do this :
00 22 * * * python /media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 30 -1 -i >> /media/Store/galaxy/galaxy-dist/temp 2>&1
Traceback (most recent call last): File "/media/Store/galaxy/galaxy-dist/scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> from galaxy import eggs ImportError: No module named galaxy
Note that I am directing the output to a file only to try to find out why it's not working.
Is this a problem with environment?
Any suggestions what to try would be much appreciated.
Regards
James
J P Mullan
participants (2)
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Geert Vandeweyer -
James Mullan