Re: [galaxy-dev] Exiting a java application without errors
Hi;
My interpretation is that your BioJava tool is sending normal
information to stderr, and Galaxy interprets it as an error. The same
happened to me with OPPL-Galaxy.
This is a well known bug
(http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr). You
have two options:
- Best option: Use a wrapper as described in the page just mentioned.
- Worse option: use UNIX redirection to redirect the stderr output of
your tool to /dev/null. This is much quicker and easier to implement,
but it is a bad solution since legit errors of your BioJava tool will be
simply ignored (The process will simply stop). Something like this in
your tool XML:
commandjava -jar ${__tool_data_path__}/shared/jars/your_tool.jar
$input $output 2/dev/null/command
Cheers
On az., 2011.eko aberen 21a 18:53, graham etherington (TSL) wrote:
Hi,
I've created a java app tested it from the command line and put it in the
shared/jars folder. It runs for a while and then the history item turns
red. If I view the dataset output though, everything is as should be, i.e.
the expected output from the tool is seen.
If I click on the view error 'bug' this is what I see:
Tool execution generated the following error message:
21-Dec-2011 17:08:14
org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading
/home/galaxy/software/galaxy-central/database/files/012/dataset_12450.dat
This is the output from org.biojava3.genome.parsers.gff and I have no way
of switching that off.
Can anyone suggest a way to handle this output so that it doesn't throw an
error. I need the output from this tool to use as input to other tools.
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
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--
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com
Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/
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Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
On 12/22/2011 11:46 AM, liram_va...@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:h...@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-...@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_va...@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:h...@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_va...@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
Re: [galaxy-dev] Itinerary for 10/24 UVa visit
The tool shed does not handle displaying images included in tool configs like
this, nor does it properly link to other files that within the tool's
subdirectory hierarchy to which the tool config may point. This is because the
files are contained within an hg repository's internal .i files, and the
process of deciphering the relative pointer, opening and reading the file and
displaying it correctly is non-trivial.
The tool shed displays most of the tool though, so the user looking at it is
provided an overall general sense of what the tool does. Those developing
tools that plan to host them on the tool shed should develop them as usual, not
making decisions for the tool page based on what will or will not be correctly
displayed in the tool shed.
At some point I may make some improvements in this area, but it is nowhere on
my development plans at the current time.
On Dec 21, 2011, at 8:29 PM, James Taylor wrote:
Hrm... Don't know if we have a solution in the Toolshed for this yet.
Greg, thoughts? Thanks!
-- jt
(composed on my phone)
On Dec 21, 2011, at 5:56 PM, Aaron Quinlan aaronquin...@gmail.com wrote:
Okay, last question for the day. For some of the more complicated tools,
I'd like to include a little PNG image as an example. I noticed that the
gops XML files use references like:
.. image:: ./static/operation_icons/gops_complement.gif
However, I imagine you want something slightly different for Tool Shed
tools. I couldn't find any docs on this - how should I setup my repository
directory structure for using icons in the XML files?
Sorry to bother...
arq
On Dec 21, 2011, at 1:37 PM, James Taylor wrote:
Excellent!
On Dec 21, 2011, at 1:31 PM, Aaron Quinlan wrote:
Works like a charm. Hoping to have a few tools up on the shed by the
New Year. Speaking of, have a good one.
On Dec 21, 2011, at 12:58 PM, James Taylor wrote:
Aaron, right now Galaxy instances don't come with all the len files in
the distribution, there is a cron script to generate them from UCSC
tables.
Frankly, that is gross, I'm thinking we should do that once ourselves,
keep it version controlled, and let people rsync it down.
But in the meantime, drop hg19.len in tool-data/shared/ucsc/chrom and you
should be good to go.
On Dec 21, 2011, at 12:51 PM, Aaron Quinlan wrote:
Hey James,
I am putting the finishing touches on a first small release of bedtools
on the tool shed. However, I am facing one likely trivial problem.
GenomeCoverageBed, when accepting BED input, needs to know the
chromosome sizes in order to do its work. On the command line, this
done by passing it a chromSizes file as a -g option. However, I believe
Galaxy can be told which genome one is dealing with for a given file.
In turn, I imagine I can automatically point the tool to the correct
chromSizes file without having the user explicitly say which file to
use.
I guessed that this is what complement.xml was doing with the -l
${chromInfo} $allchroms call.
However, I can't get this to work. When I added ${chromInfo} as the -g
option for genomeCoverageBed, it complained that it couldn't find
hg19.len.
Can you point me to a link for how to do this? I imagine I am missing
something obvious.
Best,
Aaron
On Dec 1, 2011, at 10:46 AM, James Taylor wrote:
On Nov 30, 2011, at 8:18 PM, Aaron Quinlan wrote:
So, I plan to just release XML configs and assume the user has
installed the correct version until the fabric script support is
present.
This is definitely the way to go.
It'll happen. I hope things are going well.
Okay, but do let me know if I can help.
-- jt
James Taylor, Assistant Professor, Biology / Computer Science, Emory
University
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
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Re: [galaxy-dev] Exiting a java application without errors
The first option (wrapper) also gives one the opportunity to actually check for
errors.
Chris
On Dec 22, 2011, at 2:21 AM, Mikel Egaña Aranguren meg...@fi.upm.es wrote:
Hi;
My interpretation is that your BioJava tool is sending normal information to
stderr, and Galaxy interprets it as an error. The same happened to me with
OPPL-Galaxy.
This is a well known bug
(http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr). You have
two options:
- Best option: Use a wrapper as described in the page just mentioned.
- Worse option: use UNIX redirection to redirect the stderr output of your
tool to /dev/null. This is much quicker and easier to implement, but it is a
bad solution since legit errors of your BioJava tool will be simply ignored
(The process will simply stop). Something like this in your tool XML:
commandjava -jar ${__tool_data_path__}/shared/jars/your_tool.jar $input
$output 2/dev/null/command
Cheers
On az., 2011.eko aberen 21a 18:53, graham etherington (TSL) wrote:
Hi,
I've created a java app tested it from the command line and put it in the
shared/jars folder. It runs for a while and then the history item turns
red. If I view the dataset output though, everything is as should be, i.e.
the expected output from the tool is seen.
If I click on the view error 'bug' this is what I see:
Tool execution generated the following error message:
21-Dec-2011 17:08:14
org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading
/home/galaxy/software/galaxy-central/database/files/012/dataset_12450.dat
This is the output from org.biojava3.genome.parsers.gff and I have no way
of switching that off.
Can anyone suggest a way to handle this output so that it doesn't throw an
error. I need the output from this tool to use as input to other tools.
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
___
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/
--
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com
Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
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 h...@fmi.ch wrote: On 12/22/2011 11:46 AM, liram_va...@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:h...@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-...@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_va...@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:h...@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_va...@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
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_va...@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:cjfie...@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-...@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 Hotzh...@fmi.ch wrote: On 12/22/2011 11:46 AM, liram_va...@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:h...@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-...@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_va...@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
Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
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:h...@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-...@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_va...@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:h...@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_va...@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:j...@bx.psu.edu] Sent:
Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
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:h...@fmi.ch] Sent: Thursday, December 22, 2011 5:26 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: cjfie...@illinois.edu; galaxy-...@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_va...@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:cjfie...@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-...@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 Hotzh...@fmi.ch wrote: On 12/22/2011 11:46 AM, liram_va...@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
[galaxy-dev] Stuck at Job is waiting to run when using Get data
Dear Galaxy team: I was trying to use the Get Data - Upload File tool yesterday. I uploaded all files through FTP. Then selected them in Files uploaded via FTP, selected auto-detect + Mouse July 2007 (NCBI37/mm9) (mm9) and clicked execute. My jobs are registered, but they all stuck at Job is waiting to run. I waited for over 16 hours and they are still showing Job is waiting to run. I tried to click Run the job again and it says Could not find the job for this dataset. I tried to delete all the jobs, log out and log in. Then add jobs again, but still no luck, they all still stuck at Job is waiting to run. My data files are 8 x 3Gb sized fastq files. Please help. Liangz ___ 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/
Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
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_va...@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:cjfie...@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-...@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 Hotzh...@fmi.ch wrote: On 12/22/2011 11:46 AM, liram_va...@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:h...@fmi.ch] Sent: Wednesday, December 21, 2011 4:59 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: galaxy-...@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_va...@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:h...@fmi.ch] Sent: Monday, December 19, 2011 7:01 PM To: VARDI,LIRAM
Re: [galaxy-dev] running two Galaxy installations on one server - was: Re: Can not clean my galaxy datasets
On 12/22/2011 09:57 AM, amir_ben-...@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:h...@fmi.ch] Sent: Thursday, December 22, 2011 5:26 PM To: VARDI,LIRAM (A-Labs,ex1) Cc: cjfie...@illinois.edu; galaxy-...@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_va...@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:cjfie...@illinois.edu] Sent: Thursday, December 22, 2011 4:50 PM To: Hans-Rudolf Hotz Cc: VARDI,LIRAM (A-Labs,ex1); galaxy-...@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 Hotzh...@fmi.ch wrote: On 12/22/2011 11:46 AM, liram_va...@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
