Can not clean my galaxy datasets
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scali... But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Liram This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database. Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out. Regards, Hans Have you tried to run a On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scali...
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Hans, Thank you for your quick reply. Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance! Liram -----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets Hi Liram This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database. Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out. Regards, Hans Have you tried to run a On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application% 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Liram I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system. for the installation procedure, see: http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation. Regards, Hans On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application% 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Hans, Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems. Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port. 3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line". The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message: URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158] I suppose that the problem is again caused due to collision between the databases. But how can I separate between them? Thanks you!! Liram -----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets Hi Liram I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system. for the installation procedure, see: http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation. Regards, Hans On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved? Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other. Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
Hi Hans, Sorry, but I not familiar with type of the database that Galaxy is running and didn't configure any of the Galaxy SQL features. (In another words, I don't have a clue what is PostgreSQL or SQLite and how to configure it... :-) ) About your suggestion: You absolutely right. I tried to install and run another Galaxy server and nothing else besides this, And still, the same problem is coming up when using two Galaxy instances. Thank you for your time and help, Liram -----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Thursday, December 22, 2011 2:09 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved? Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other. Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicatio n % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate. Chris On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz" <hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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:
Hi Chris, Thank you. Just to make sure that I fully understand: Basically you say that there are no easy way to run two Galaxy process on the same Linux operating system? Thanks, Liram -----Original Message----- From: Fields, Christopher J [mailto:cjfields@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate. Chris On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz" <hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicati on % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote:
Hello,
My name is Liram Vardi and I'm using local Galaxy instance.
Anyway, I can't clean my deleted datasets from my own locally disk.
When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
First, I used the "delete 'X' icon" near the dataset to delete the dataset,
Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list
with the note: /"This dataset has been deleted. Click _here_ to undelete it"//*but I don't get the also the option "or _here_ to immediately remove it from disk."*/.
Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and
my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list.
I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset.
What is the problem?
Thanks a lot for your help!
Liram
___________________________________________________________ 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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 12/22/2011 04:13 PM, liram_vardi@agilent.com wrote:
Hi Chris,
Thank you. Just to make sure that I fully understand: Basically you say that there are no easy way to run two Galaxy process on the same Linux operating system?
Hi Liram I am sorry, but I can't leave this statement out there without strongly objecting! I have been running up to 5 Galaxy servers (one production and four test servers) on the same box without any problems. It is difficult to help you remotely, with only seeing snippets from your errors. But I am sure your local sysadmin can help you setting up the relational databases and making sure the file systems for your two servers are really separate from each other. Hans
Thanks, Liram
-----Original Message----- From: Fields, Christopher J [mailto:cjfields@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate.
Chris
On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz"<hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicati on % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote: > Hello, > > My name is Liram Vardi and I'm using local Galaxy instance. > > Anyway, I can't clean my deleted datasets from my own locally disk. > > When I am trying to delete dataset, as was explained in > http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, > > First, I used the "delete 'X' icon" near the dataset to delete > the dataset, > > Then, when I go to "Options -> Show Deleted Datasets", I can see > my "deleted dataset" on the list > > with the note: /"This dataset has been deleted. Click _here_ to > undelete it"//*but I don't get the also the option "or _here_ to > immediately remove it from disk."*/. > > Also, when I use the option "Options -> Purge Deleted Datasets", > I'm getting a message "0 datasets have been deleted permanently" > and > > my deleted dataset still stays in the "Options -> Show Deleted Datasets" > menu list. > > I also tried to clear the history, but when I'm doing that, the > "using X Mb" tab on the upper right corner is still not reset. > > What is the problem? > > Thanks a lot for your help! > > Liram > > > > ___________________________________________________________ > 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/
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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:
Hi Hans, Thank you again on your prompt answer. From your reply below, it is clear that it should be possible to run multiple Galaxy servers under a single linux - this is exactly what we are trying to do: running two galaxy servers (one production one for test). I would think this is relatively common scenario (i.e., setting up two servers), so it might be a good idea to figure out and post instructions on the wiki how to achieve this. We are really novice with regards to the linux OS (installed it within a 'virtualbox' just to be able to run the galaxy server) - so there is no local linux sysadmin to consult (or someone that knows how to work with the database). We were hoping it would be relatively easy process to setup a galaxy server, perhaps we were too naïve... We do not understand the collision between the two instances, as they were installed in two different locations altogether (the production server is under '/home/liram/sdb1/galaxy-dist', and the test server is under'/home/liram/test/galaxy-dist') . Somehow, it seems that the two server do try to access some shared resource - we have no clue what is the shared resource and how to fix this. Let us know if there is some log file or additional information we can send you as we are completely stuck now :-( Thanks again for your help, Amir Ben-Dor -----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Thursday, December 22, 2011 5:26 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: cjfields@illinois.edu; galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets On 12/22/2011 04:13 PM, liram_vardi@agilent.com wrote:
Hi Chris,
Thank you. Just to make sure that I fully understand: Basically you say that there are no easy way to run two Galaxy process on the same Linux operating system?
Hi Liram I am sorry, but I can't leave this statement out there without strongly objecting! I have been running up to 5 Galaxy servers (one production and four test servers) on the same box without any problems. It is difficult to help you remotely, with only seeing snippets from your errors. But I am sure your local sysadmin can help you setting up the relational databases and making sure the file systems for your two servers are really separate from each other. Hans
Thanks, Liram
-----Original Message----- From: Fields, Christopher J [mailto:cjfields@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate.
Chris
On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz"<hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port.
It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicati on % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote: > Hello, > > My name is Liram Vardi and I'm using local Galaxy instance. > > Anyway, I can't clean my deleted datasets from my own locally disk. > > When I am trying to delete dataset, as was explained in > http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, > > First, I used the "delete 'X' icon" near the dataset to delete > the dataset, > > Then, when I go to "Options -> Show Deleted Datasets", I can see > my "deleted dataset" on the list > > with the note: /"This dataset has been deleted. Click _here_ to > undelete it"//*but I don't get the also the option "or _here_ to > immediately remove it from disk."*/. > > Also, when I use the option "Options -> Purge Deleted Datasets", > I'm getting a message "0 datasets have been deleted permanently" > and > > my deleted dataset still stays in the "Options -> Show Deleted Datasets" > menu list. > > I also tried to clear the history, but when I'm doing that, the > "using X Mb" tab on the upper right corner is still not reset. > > What is the problem? > > Thanks a lot for your help! > > Liram > > > > ___________________________________________________________ > 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/
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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 12/22/2011 09:57 AM, amir_ben-dor@agilent.com wrote:
Hi Hans,
Thank you again on your prompt answer. From your reply below, it is clear that it should be possible to run multiple Galaxy servers under a single linux - this is exactly what we are trying to do: running two galaxy servers (one production one for test). I would think this is relatively common scenario (i.e., setting up two servers), so it might be a good idea to figure out and post instructions on the wiki how to achieve this.
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy Note under 'Basic Configuration'.
We are really novice with regards to the linux OS (installed it within a 'virtualbox' just to be able to run the galaxy server) - so there is no local linux sysadmin to consult (or someone that knows how to work with the database). We were hoping it would be relatively easy process to setup a galaxy server, perhaps we were too naïve... Maybe a virtualbox-specific configuration issue, e.g. specify resources available to the VM. Is there a limit on mem, CPU, open ports, etc? We do not understand the collision between the two instances, as they were installed in two different locations altogether (the production server is under '/home/liram/sdb1/galaxy-dist', and the test server is under'/home/liram/test/galaxy-dist') . Somehow, it seems that the two server do try to access some shared resource - we have no clue what is the shared resource and how to fix this. Are you sure you have separate directories specifies with Apache? For instance, are both configured as the web server root (see link above)? Let us know if there is some log file or additional information we can send you as we are completely stuck now :-(
Thanks again for your help,
Amir Ben-Dor As Hans implied, might be nice to see how you configured Apache and Galaxy.
chris
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Thursday, December 22, 2011 5:26 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: cjfields@illinois.edu; galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
On 12/22/2011 04:13 PM, liram_vardi@agilent.com wrote:
Hi Chris,
Thank you. Just to make sure that I fully understand: Basically you say that there are no easy way to run two Galaxy process on the same Linux operating system?
Hi Liram
I am sorry, but I can't leave this statement out there without strongly objecting!
I have been running up to 5 Galaxy servers (one production and four test servers) on the same box without any problems.
It is difficult to help you remotely, with only seeing snippets from your errors. But I am sure your local sysadmin can help you setting up the relational databases and making sure the file systems for your two servers are really separate from each other.
Hans
Thanks, Liram
-----Original Message----- From: Fields, Christopher J [mailto:cjfields@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate.
Chris
On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz"<hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port. It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote: > Hi Jennifer, > > Thank you again for the quick reply in my last issue. > > I have another Galaxy problem and I hope you will be able to assist. > Because I am developing my Galaxy server while there are members > in my group that are using this Galaxy instance in parallel, I am > trying to create another Galaxy process (instance), which will be > used only for testing... > > Therefore, I created a copy of Galaxy directory in other location > (let > say: /galaxy-dist_test) > And changed the listening port in "universe_wsgi.ini" to another > port (8081). > Then, I tried to run both of Galaxy instances in parallel. > (One is listening on port 8080 and the other is on 8081) > > The problem is occurred when I send a job for a run in one of the > instance (let say: the one that run on 8080), Then, It cause to > the another Instance (the one on port 8081) to collapse (And the > history is disappeared...) > > What is the problem? > How can I solve it? > How can I create two different and self-contained galaxy servers > on the same computer? > > I tried also to use the instructions : > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicati > on > % > 20Scaling > > But it was not helpful to my problem... > > Thank you a lot! > Liram > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Tuesday, November 29, 2011 4:42 PM > To: VARDI,LIRAM (A-Labs,ex1) > Cc: galaxy-dev@bx.psu.edu > Subject: Re: [galaxy-dev] Can not clean my galaxy datasets > > Hello Liram, > > Perhaps the allow_user_dataset_purge option has not been set to > True in universe_wsgi.ini? > > Please see this wiki for details: > http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas > > Hopefully this helps, but please let us know if you need more > assistance, > > Best, > > Jen > Galaxy team > > On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote: >> Hello, >> >> My name is Liram Vardi and I'm using local Galaxy instance. >> >> Anyway, I can't clean my deleted datasets from my own locally disk. >> >> When I am trying to delete dataset, as was explained in >> http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, >> >> First, I used the "delete 'X' icon" near the dataset to delete >> the dataset, >> >> Then, when I go to "Options -> Show Deleted Datasets", I can see >> my "deleted dataset" on the list >> >> with the note: /"This dataset has been deleted. Click _here_ to >> undelete it"//*but I don't get the also the option "or _here_ to >> immediately remove it from disk."*/. >> >> Also, when I use the option "Options -> Purge Deleted Datasets", >> I'm getting a message "0 datasets have been deleted permanently" >> and >> >> my deleted dataset still stays in the "Options -> Show Deleted Datasets" >> menu list. >> >> I also tried to clear the history, but when I'm doing that, the >> "using X Mb" tab on the upper right corner is still not reset. >> >> What is the problem? >> >> Thanks a lot for your help! >> >> Liram >> >> >> >> ___________________________________________________________ >> 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/ > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support >
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:
No, I'm sure it's possible. I can't say how easy it is, I've never tested it myself, but I would assume one could use virtual hosts or something similar. I personally just like keeping such things as separate as possible, and having them as separate VMs makes it a little easier to distinctly maintain each. chris On 12/22/2011 09:13 AM, liram_vardi@agilent.com wrote:
Hi Chris,
Thank you. Just to make sure that I fully understand: Basically you say that there are no easy way to run two Galaxy process on the same Linux operating system?
Thanks, Liram
-----Original Message----- From: Fields, Christopher J [mailto:cjfields@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
We are anticipating a similar issue and decided it would be easier to just have separate VMs where possible. I know this isn't always possible, but it is a very easy way to both manage multiple galaxy instances and keep the various galaxy instances completely separate.
Chris
On Dec 22, 2011, at 6:10 AM, "Hans-Rudolf Hotz"<hrh@fmi.ch> wrote:
On 12/22/2011 11:46 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your reply. Anyway, I tried to install Galaxy again by using the site "check-out" (hg clone https://...) and it still cause problems.
Specifically, those were my steps: 1) I Installed galaxy in different location. 2) After run run.sh in the first time, I changed universe_wsgi.ini to listen on different port. It is hard to believe that your new test installation running with SQLite interferes with your existing installation running with PostgreSQL(?). Are you sure, there is not a third 'party' involved?
Also, I would stop at this step (ie: changed universe_wsgi.ini to listen on different port) and run your installation first like this. And wait with copying anything from the exiting code or data or directories. Till you manage to get the two web site to run in parallel without interfering with each other.
Regards, Hans
3) Manually, I copied "tools" and "tool-data" directories from the old instance of Galaxy to the new location (In order to get my new tools). 4) Also, I copied the old config tool file: " tool_conf.xml" 5) Then, Run the new Galaxy instance. In parallel, the old Galaxy is already "on line".
The problem is that any operation on the new Galaxy instance cause to the other Galaxy to Throw the following error message:
URL: http://<ip address>.../user/login?use_panels=False File '/home/liram/sdb1/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/liram/sdb1/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) . . . . File '/home/liram/sdb1/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked u'UPDATE galaxy_session SET update_time=?, is_valid=? WHERE galaxy_session.id = ?' ['2011-12-22 10:27:05.978992', 0, 158]
I suppose that the problem is again caused due to collision between the databases. But how can I separate between them?
Thanks you!! Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu; BEN-DOR,AMIR (A-Labs,ex1) Subject: running two Galaxy installations on one server - was: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
I was suggesting: instead of copying the existing Galaxy directory into another location. Download and install a new Galaxy installation in a separate location on your file system.
for the installation procedure, see:
http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy
all you need to do in the new installation is changing the port number. It will create its own file system and by default it will use its own SQLite database. Hence, there should be no interference with your existing, production Galaxy installation.
Regards, Hans
On 12/21/2011 09:16 AM, liram_vardi@agilent.com wrote:
Hi Hans,
Thank you for your quick reply.
Sorry, But I'm a "rookie" Galaxy user, So may you pls explain me in details the meaning by " running a second Galaxy server in parallel using a fresh check-out "? Thank a lot for your assistance!
Liram
-----Original Message----- From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: Jennifer Jackson; Galaxy Dev; BEN-DOR,AMIR (A-Labs,ex1) Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hi Liram
This sounds like the two Galaxy server use the same (PostgreSQL/MySQL) database.
Before copying your existing Galaxy server, you might wanna start with running a second Galaxy server in parallel using a fresh check-out.
Regards, Hans
Have you tried to run a
On 12/19/2011 04:08 PM, Jennifer Jackson wrote:
On 12/19/11 6:15 AM, liram_vardi@agilent.com wrote:
Hi Jennifer,
Thank you again for the quick reply in my last issue.
I have another Galaxy problem and I hope you will be able to assist. Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel, I am trying to create another Galaxy process (instance), which will be used only for testing...
Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test) And changed the listening port in "universe_wsgi.ini" to another port (8081). Then, I tried to run both of Galaxy instances in parallel. (One is listening on port 8080 and the other is on 8081)
The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080), Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
What is the problem? How can I solve it? How can I create two different and self-contained galaxy servers on the same computer?
I tried also to use the instructions : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Applicati on % 20Scaling
But it was not helpful to my problem...
Thank you a lot! Liram
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, November 29, 2011 4:42 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram,
Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
Hopefully this helps, but please let us know if you need more assistance,
Best,
Jen Galaxy team
On 11/29/11 5:44 AM, liram_vardi@agilent.com wrote: > Hello, > > My name is Liram Vardi and I'm using local Galaxy instance. > > Anyway, I can't clean my deleted datasets from my own locally disk. > > When I am trying to delete dataset, as was explained in > http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, > > First, I used the "delete 'X' icon" near the dataset to delete > the dataset, > > Then, when I go to "Options -> Show Deleted Datasets", I can see > my "deleted dataset" on the list > > with the note: /"This dataset has been deleted. Click _here_ to > undelete it"//*but I don't get the also the option "or _here_ to > immediately remove it from disk."*/. > > Also, when I use the option "Options -> Purge Deleted Datasets", > I'm getting a message "0 datasets have been deleted permanently" > and > > my deleted dataset still stays in the "Options -> Show Deleted Datasets" > menu list. > > I also tried to clear the history, but when I'm doing that, the > "using X Mb" tab on the upper right corner is still not reset. > > What is the problem? > > Thanks a lot for your help! > > Liram > > > > ___________________________________________________________ > 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
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participants (6)
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amir_ben-dor＠agilent.com -
Chris Fields -
Fields, Christopher J
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Hans-Rudolf Hotz -
Jennifer Jackson -
liram_vardi＠agilent.com