repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
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:
Lukasz-
How are you stopping the process? It's possible that the python task for galaxy is still running. I would recommend trying to send a "kill" signal to that process. Something like "kill -9 PID", where PID is the process id for galaxy, should work.
-Scott
----- Original Message -----
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
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:
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:
Galaxy should probably be shutdown with --stop-daemon (depending on how you are running it).
In the future we can look at making the logging handle the HUP signal.
-- jt
On Tue, Sep 25, 2012 at 11:40 AM, Scott McManus scottmcmanus@gatech.edu wrote:
Lukasz-
How are you stopping the process? It's possible that the python task for galaxy is still running. I would recommend trying to send a "kill" signal to that process. Something like "kill -9 PID", where PID is the process id for galaxy, should work.
-Scott
----- Original Message -----
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
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:
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:
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:
I use start-stop-daemon that sends SIGTERM (which is a default signal sent to a service that is being asked to stop) to Galaxy to let Galaxy store all information in a database, close files, etc., and terminate itself. When Galaxy process is terminated, both shell and python scripts (Galaxy tools) are still running.
Effects of using SIGKILL/SIGSTOP are not predictable. I do not want to risk that Galaxy does not insert entries to the database that should be inserted to start Galaxy correctly again, or does not flush buffers to write all data to files and close the files correctly.
Thanks, Lukasz
On 9/25/12 10:40 AM, Scott McManus wrote:
Lukasz-
How are you stopping the process? It's possible that the python task for galaxy is still running. I would recommend trying to send a "kill" signal to that process. Something like "kill -9 PID", where PID is the process id for galaxy, should work.
-Scott
----- Original Message -----
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
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:
On Sep 25, 2012, at 6:57 AM, Lukasz Lacinski wrote:
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
I am not sure about multiple galaxy process install, but I think a logrotate configuration with copytruncate option should work fine. For example,
{{{ /apps/galaxy/galaxy-latest/paster.log { missingok rotate 10 copytruncate # logrotate script should be called by a cron job and hence daily/weekly settings are not added to conf file. # 'size 1' setting ensures that log file will be rotated whenevr it is called by the cron unless size < 1 byte size 1 compress create 640 galaxy-user galaxy-group }}}
-- Shantanu
On Sep 25, 2012, at 12:35 PM, Lukasz Lacinski wrote:
I use start-stop-daemon that sends SIGTERM (which is a default signal sent to a service that is being asked to stop) to Galaxy to let Galaxy store all information in a database, close files, etc., and terminate itself. When Galaxy process is terminated, both shell and python scripts (Galaxy tools) are still running.
Effects of using SIGKILL/SIGSTOP are not predictable. I do not want to risk that Galaxy does not insert entries to the database that should be inserted to start Galaxy correctly again, or does not flush buffers to write all data to files and close the files correctly.
Hi Lukasz,
Galaxy does not terminate jobs running in the local runner when the Galaxy server stops. If you need to be able to restart the server without losing running jobs, you'll need to set up a cluster scheduler, even if it just submits jobs to the localhost.
--nate
Thanks, Lukasz
On 9/25/12 10:40 AM, Scott McManus wrote:
Lukasz-
How are you stopping the process? It's possible that the python task for galaxy is still running. I would recommend trying to send a "kill" signal to that process. Something like "kill -9 PID", where PID is the process id for galaxy, should work.
-Scott
----- Original Message -----
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
--nate
Thanks, Lukasz ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ 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:
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:
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:
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:
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and Tophat all run fine with my small subset of paired-end Illumina reads. Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2.
Three entires in my history appear (gene expression, transcript expression, and assembled transcripts) containing reasonable output. Each of these entries is highlighted red, though without the red circle with an X. The box contains the message:
An error occurred running this job: cufflinks v2.0.2 cufflinks -q --no-update-check -l 300000 -F 0.100000 -j 0.150000 -p 4 cp: cannot stat ` /home/galaxy/galaxy-dist/database/job_working_directory/000/20/global_model.txt': No such file or directory
What is this global_model.txt file and why might it be missing/have failed?
I also use a logrotate script: '/etc/logrotate.d/galaxy'
/path/to/galaxy/install/*.log { weekly rotate 52 copytruncate }
The 'compress' options seems like it might be nice, and I'm not sure of the effect of size 1. I don't think the 'create 640 galaxy-user galaxy-group' has an effect when the copytruncate option is used. For the same reason, I don't think the missingok option is needed either.
This might be a nice thing to add to the wiki at: "http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server".
Lance
On Sep 25, 2012, at 6:57 AM, Lukasz Lacinski wrote:
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
I am not sure about multiple galaxy process install, but I think a logrotate configuration with copytruncate option should work fine. For example,
{{{ /apps/galaxy/galaxy-latest/paster.log { missingok rotate 10 copytruncate # logrotate script should be called by a cron job and hence daily/weekly settings are not added to conf file. # 'size 1' setting ensures that log file will be rotated whenevr it is called by the cron unless size< 1 byte size 1 compress create 640 galaxy-user galaxy-group }}}
-- Shantanu
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:
On Oct 1, 2012, at 2:57 PM, Lance Parsons wrote:
I also use a logrotate script: '/etc/logrotate.d/galaxy'
/path/to/galaxy/install/*.log { weekly rotate 52 copytruncate }
The 'compress' options seems like it might be nice, and I'm not sure of the effect of size 1. I don't think the 'create 640 galaxy-user galaxy-group' has an effect when the copytruncate option is used. For the same reason, I don't think the missingok option is needed either.
This might be a nice thing to add to the wiki at: "http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server".
Lance
That's right. I agree that 'size 1', 'missingok' and 'create galaxy-user galaxy-group' options are practically not needed and can be excluded. As mentioned earlier, it's the copytruncate option that should be useful for rotating galaxy log files.
Also, I would like to mention that you can run logrotate program as a non-root user (galaxy-user) if your galaxy application is served from a root squash enabled NFS mount. In this case, the logrotate configuration can be put in a non-default location (/etc/logrotate.d) and can be called through non-root user's cron jobs.
-- Shantanu
On Sep 25, 2012, at 6:57 AM, Lukasz Lacinski wrote:
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory to start Galaxy. The log file
--log-file /home/galaxy/galaxy.log
specified in the script grows really quickly. How to logrotate the file?
Hi Lukasz,
I'd suggest using whatever log rotation utility is provided by your OS. You'll need to restart the Galaxy process to begin writing to the new log once the old one has been rotated.
Hi Nate,
When Galaxy is started again, it fails because it cannot bind a socket to port 8080, that is already bound by child Galaxy processes orphaned by the former Galaxy process.
When Galaxy forks to run tools, a child process does not close open files/sockets that the child process does not need.
Thanks, Lukasz
I am not sure about multiple galaxy process install, but I think a logrotate configuration with copytruncate option should work fine. For example,
{{{ /apps/galaxy/galaxy-latest/paster.log { missingok rotate 10 copytruncate # logrotate script should be called by a cron job and hence daily/weekly settings are not added to conf file. # 'size 1' setting ensures that log file will be rotated whenevr it is called by the cron unless size< 1 byte size 1 compress create 640 galaxy-user galaxy-group }}}
-- Shantanu
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:
-- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University
galaxy-dev@lists.galaxyproject.org
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