Re: [galaxy-dev] login problem (redirection to the login page)

[Makis Ladoukakis]

Hello,

I've been struggling with the login issue with Galaxy for a while now. Try to 
use "incognito mode" on your browser when accessing the url for Galaxy and see 
what happens. Also if you don't really need for your users to activate their 
accounts by e-mail set the "user_activation_on=False" in galaxy.ini. You have 
to have set up your smtp server for that which can be a fuss.

Cheers,
Makis

Date: Thu, 5 Nov 2015 18:16:56 +0100
From: floreline.touch...@gmail.com
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] login problem (redirection to the login page)

Hi,
I come back to you with some news of my login problem.
I delete my browser cache and cookies with no result. 
I restart all my services (Apache, PostgreSQL, Galaxy) with no more result.
I try to start fresh with my PostgreSQL database cluster (to clear all the user 
information). But it didn't solve the problem. When I register with a user 
name, I get : 
- on the browser side:
"Now logged in as @example.com.
Verification email has been sent to your email address. Please verify it by 
clicking the activation link in the email.
Please check your spam/trash folder in case you cannot find the message.
Return to the home page."
- on the server side :
"galaxy.util ERROR 2015-11-05 17:21:25,394 Mail is not configured for this 
Galaxy instance.
galaxy.util INFO 2015-11-05 17:21:25,394 From nobody Thu Nov  5 17:21:25 2015
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
To: @example.com
From:
Subject: Galaxy Account Activation
Hello ,
In order to complete the activation process for @example.com begun on 
11/05/15 at ip:port, please click on the following link to verify your account:
http://ip:port/activate?email=%40example.com_token=3285151b21c8f85590db0f0c1089110d934f2400
By clicking on the above link and opening a Galaxy account you are also 
confirming that you have read and agreed to Galaxy's Terms and Conditions for 
use of this service (None). This includes a quota limit of one account per 
user. Attempts to subvert this limit by creating multiple accounts or through 
any other method may result in termination of all associated accounts and data.
Please contact us if you need help with your account at: None. You can also 
browse resources available at: None.
More about the Galaxy Project can be found at galaxyproject.org
Your Galaxy Team"

I get a new entry in the galaxy_user table (PostgreSQl table) with "f" in the 
activate field. which I find logical.
If I activate the account with the link, the value becomes "t". Still logical.
But I'm redirected to the welcome page after the login and there's only the 
"login" and "register" options under the user tab.
I have no error on the server log.
For each connection attempt I can see this line : 
"galaxy.auth.providers.localdb DEBUG 2015-11-05 17:31:04,681 User: 
@example.com, LOCALDB: True
10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "POST /user/login?use_panels=False 
HTTP/1.1" 200 - "http://ip:port/user/login; "Mozilla/5.0 (Windows NT 6.1; 
rv:39.0) Gecko/20100101 Firefox/39.0"
10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "GET /root HTTP/1.1" 200 - 
"http://ip:port/user/login?use_panels=False; "Mozilla/5.0 (Windows NT 6.1; 
rv:39.0) Gecko/20100101 Firefox/39.0"
10.80.6.195 - - [05/Nov/2015:17:31:05 +0200] "GET /root/welcome HTTP/1.1" 302 - 
"http://ip:port/root; "Mozilla/5.0 (Windows NT 6.1; rv:39.0) Gecko/20100101 
Firefox/39.0"
"
Is it normal ?
My postgreSQl database seems to work fine.
It doesn't come from a browser cache issue (I clear mine and I try to login to 
Galaxy with another computer on the same network).
Or are there other caches I should be aware of ?
Is there another way to get an operational application ? And where did this 
issue come from ? I'm only testing the application but it surprises me since I 
had a working instance for few months. 
Thanks in advance,
F.T


2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD :
Update :When I clic several time on the galaxy name, I got this on the log : 
Exception happened during processing of request from ('127.0.0.1', 45055)
Traceback (most recent call last):
  File path/to/galaxy-master/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", 
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
 
2015-11-04 15:09 GMT+01:00 Floreline TOUCHARD :
Here is some details :when I enable the access to Galaxy without authentication 
I'm 

Re: [galaxy-dev] FASTQ Groomer tool

[Martin Čech]

Hi Edgar,

it seems you are hitting this fail:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/handler.py#L124
which
hints that the tool is not properly loaded in the toolbox. Did you restart
the server and handlers after you installed the tool?
I cannot help with the MySQL as we do not usually test or run Galaxy on it.
I understand that you did not update your Galaxy for 6 months?

Thank you for using Galaxy.

Martin

On Thu, Nov 5, 2015 at 2:20 PM Fernandez Edgar 
wrote:

> Hello again,
>
>
>
> I installed today the tool : fastq_all_to_sanger
>
> I get the same SQL error with that one too.
>
> Any ideas guys?
>
>
>
> Thank you!!!
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Fernandez Edgar
> *Envoyé :* November-04-15 8:58 AM
> *À :* 'galaxy-...@bx.psu.edu'
> *Objet :* [galaxy-dev] FASTQ Groomer tool
>
>
>
> Hello gents,
>
>
>
> I just installed "FASTQ Groomer tool" for the teachers to try it out and
> I’ve been getting the following error than I do not understand:
>
>
>
> galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job
> is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756
>
> galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool '
> toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4'
> removed from tool config, unable to run job
>
> galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756
>
> Traceback (most recent call last):
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in
> __monitor_step
>
> job_state = self.__check_job_state( job )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in
> __check_job_state
>
> state, job_destination = self.__verify_job_ready( job, job_wrapper )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in
> __verify_job_ready
>
> job_wrapper.fail( e )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984,
> in fail
>
> self.sa_session.flush()
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150,
> in do
>
> return getattr(self.registry(), name)(*args, **kwargs)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2004, in flush
>
> self._flush(objects)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2122, in _flush
>
> transaction.rollback(_capture_exception=True)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line
> 60, in __exit__
>
> compat.reraise(exc_type, exc_value, exc_tb)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2086, in _flush
>
> flush_context.execute()
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line
> 373, in execute
>
> rec.execute(self)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line
> 532, in execute
>
> uow
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line
> 170, in save_obj
>
> mapper, table, update)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line
> 673, in _emit_update_statements
>
> execute(statement, multiparams)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914,
> in execute
>
> return meth(self, multiparams, params)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line
> 323, in _execute_on_connection
>
> return connection._execute_clauseelement(self, multiparams, params)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1010, in _execute_clauseelement
>
> compiled_sql, distilled_params
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1146, in _execute_context
>
> context)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1332, in _handle_dbapi_exception
>
> exc_info
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199,
> in raise_from_cause
>
> reraise(type(exception), exception, tb=exc_tb)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1139, in _execute_context
>
> context)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line
> 442, in do_execute
>
> cursor.execute(statement, parameters)
>
>   File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173,
> in execute
>
> self.errorhandler(self, exc, value)
>
>   File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line
> 36, in defaulterrorhandler
>
> raise errorclass, errorvalue
>
> ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an
> error in your SQL syntax; check the manual that corresponds to your MySQL
> server version for the right syntax to use near '), blurb='tool error'
> WHERE history_dataset_association.id = 1498' at line 1") [SQL: u'UPDATE
> 

Re: [galaxy-dev] FASTQ Groomer tool

[Martin Čech]

Hi Edgar,

Galaxy loads tools on start so if you install a tool it will show it in the
panel (because that config is independent and already updated) however the
toolbox will not have it yet until the restart.

I updated the wiki (
https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to
make it more clear.

Thank you for using Galaxy.

M.

On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar 
wrote:

> Hello Nicola and Martin,
>
>
>
> The service galaxy restart worked.
>
> Can you guys give me a small explanation please?
>
> Just for my understanding…
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Nicola Soranzo [mailto:nicola.sora...@gmail.com] *De la part de*
> Nicola Soranzo
> *Envoyé :* November-05-15 2:33 PM
> *À :* Fernandez Edgar; galaxy-...@bx.psu.edu
> *Objet :* Re: [galaxy-dev] FASTQ Groomer tool
>
>
>
> Hi Edgar,
> you can try to restart Galaxy (both web and handler processes) and re-run
> the tool.
>
> Cheers,
> Nicola
>
> On 05/11/15 19:18, Fernandez Edgar wrote:
>
> Hello again,
>
>
>
> I installed today the tool : fastq_all_to_sanger
>
> I get the same SQL error with that one too.
>
> Any ideas guys?
>
>
>
> Thank you!!!
>
>
>
> Cordialement / Regards,
>
> Edgar Fernandez
>
>
>
> *De :* Fernandez Edgar
> *Envoyé :* November-04-15 8:58 AM
> *À :* 'galaxy-...@bx.psu.edu'
> *Objet :* [galaxy-dev] FASTQ Groomer tool
>
>
>
> Hello gents,
>
>
>
> I just installed "FASTQ Groomer tool" for the teachers to try it out and
> I’ve been getting the following error than I do not understand:
>
>
>
> galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job
> is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756
>
> galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool '
> toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4'
> removed from tool config, unable to run job
>
> galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756
>
> Traceback (most recent call last):
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in
> __monitor_step
>
> job_state = self.__check_job_state( job )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in
> __check_job_state
>
> state, job_destination = self.__verify_job_ready( job, job_wrapper )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in
> __verify_job_ready
>
> job_wrapper.fail( e )
>
>   File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984,
> in fail
>
> self.sa_session.flush()
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150,
> in do
>
> return getattr(self.registry(), name)(*args, **kwargs)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2004, in flush
>
> self._flush(objects)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2122, in _flush
>
> transaction.rollback(_capture_exception=True)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line
> 60, in __exit__
>
> compat.reraise(exc_type, exc_value, exc_tb)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line
> 2086, in _flush
>
> flush_context.execute()
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line
> 373, in execute
>
> rec.execute(self)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line
> 532, in execute
>
> uow
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line
> 170, in save_obj
>
> mapper, table, update)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line
> 673, in _emit_update_statements
>
> execute(statement, multiparams)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914,
> in execute
>
> return meth(self, multiparams, params)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line
> 323, in _execute_on_connection
>
> return connection._execute_clauseelement(self, multiparams, params)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1010, in _execute_clauseelement
>
> compiled_sql, distilled_params
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1146, in _execute_context
>
> context)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1332, in _handle_dbapi_exception
>
> exc_info
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199,
> in raise_from_cause
>
> reraise(type(exception), exception, tb=exc_tb)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line
> 1139, in _execute_context
>
> context)
>
>   File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line
> 442, in do_execute
>
> cursor.execute(statement, parameters)
>
>   File 

Re: [galaxy-dev] Galaxy Startup Failing

[Will Holtz]

Hi Keith,

I use start-stop-daemon to launch python and I pass --chuid and --group to
start-stop-daemon so that galaxy does not run as root. It is my
understanding that start-stop-daemon creates the pid file as root before
changing user, as my /var/run/galaxy.pid is owned by root:root. I have
attached my /etc/init.d/galaxy script. This is from a Ubuntu 12.04 system.

-Will



On Wed, Nov 4, 2015 at 8:13 AM, Suderman Keith 
wrote:

> Hi Will,
>
> I tried that and it didn’t work for me.  Are you using start-stop-daemon
> to launch python?  Or do you run “python scripts/paster.py serve” from
> /etc/init.d/galaxy?
>
> If I use start-stop-daemon then python does not seem to be picking up the
> .venv.  I suspect it has something to do with .venv/bin/activate being
> sourced as root in one process and then python running as the galaxy user
> in another process.
>
> If I run “python scripts/paster.py serve” in the /etc/init.d/galaxy script
> then Galaxy is running as the root user and this is (will be) a production
> server so that is not an option.
>
> If I run python as the galaxy user from the /etc/init.d/galaxy script then
> I am back to the problem of python not being able to write to
> /var/run/galaxy.pid
>
> Keith
>
> On Nov 3, 2015, at 7:39 PM, Will Holtz  wrote:
>
> Hi Keith,
>
> I've dealt with similar situations by adding the sourcing of
> .venv/bin/activate to the etc/init.d/galaxy script. Then none of the
> pre-existing pid code needs to be changed.
>
> -Will
>
>
> On Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith 
> wrote:
>
>> The solution was rather simple, once I figured it out.
>>
>> The /etc/init.d/galaxy script was invoking scripts/paster.py script
>> directly so .venv/bin/activate was not being sourced.  The solution was to
>> modify /etc/init.d/galaxy to call a startup script that sourced
>> .venv/bin/activate before starting Galaxy.  I can write my solution up in
>> more detail, but now I am having some problems setting the pid file
>> correctly.
>>
>> If I use the --make-pidfile and --pidfile options for start-stop-daemon
>> in /etc/init.d/galaxy then /var/run/galaxy.pid contains the pid of the
>> startup script and not the pid of the Galaxy instance.
>>
>> If I try to set the pid in the startup script Galaxy won't start as the
>> script (now running as the Galaxy user) can't create/write the
>> /var/run/galaxy.pid file.
>>
>> My hack-around has been to touch the pid file (in case it doesn't exist)
>> and then chown it to the galaxy user in /etc/init.d/galaxy, but this
>> doesn't strike me as the correct way to do this.  Do any sysadmin gurus
>> have any better suggestions?
>>
>> Cheers,
>> Keith
>>
>> > On Nov 1, 2015, at 9:31 PM, Keith Suderman 
>> wrote:
>> >
>> > Greetings,
>> >
>> > I am trying to upgrade our Galaxy instance to the latest stable code
>> from master and now our instance won't start using my /etc/init.d/galaxy
>> script.  That is:
>> >
>> >> sudo service galaxy start
>> >
>> > no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't
>> running and nothing is written to the log. I am using the init.d script
>> from simison [1], which is basically the same as the one posted to the
>> Galaxy wiki [2], both of which are quite old.
>> >
>> > Galaxy does start with:
>> >
>> >> sudo su galaxy
>> >> ./run.sh --daemon
>> >
>> > so I have left Galaxy running in a screen session for now, but that is
>> less than ideal.
>> >
>> > I suspect something to do with the .venv as `./run.sh --skip-venv` also
>> fails and I don't recall Galaxy being that finicky about a venv being
>> active. Does anyone know how I can get the /etc/init.d/galaxy script (i.e.
>> start-stop-daemon) to activate the venv for paster.py?
>> >
>> > Cheers,
>> > Keith
>> >
>> > 1. http://simison.com/brian/GalaxyAdmin_notes.html
>> > 2.
>> https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
>> >
>> > --
>> > Research Associate
>> > Department of Computer Science
>> > Vassar College
>> > Poughkeepsie, NY
>> >
>> >
>> > ___
>> > 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:
>> >  https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >  http://galaxyproject.org/search/mailinglists/
>>
>> ___
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> --
> The information contained in this 

[galaxy-dev] R: Re: FASTQ Groomer tool

[Nicola Soranzo]

Hi Edgar,
to add to Martin's explanation, it is my understanding that only the web 
process from which the tool installation is initiated knows about the new tool. 
The other web and handler processes will know about it only after a restart. 

Cheers, 
Nicola 

 Martin Čech ha scritto 

>Hi Edgar,
>
>
>Galaxy loads tools on start so if you install a tool it will show it in the 
>panel (because that config is independent and already updated) however the 
>toolbox will not have it yet until the restart.
>
>
>I updated the wiki 
>(https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to 
>make it more clear.
>
>
>Thank you for using Galaxy.
>
>
>M.
>
>On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar  
>wrote:
>
>Hello Nicola and Martin,
>
> 
>
>The service galaxy restart worked.
>
>Can you guys give me a small explanation please?
>
>Just for my understanding…
>
> 
>
>Cordialement / Regards, 
>
>Edgar Fernandez
>
> 
>
>De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola 
>Soranzo
>Envoyé : November-05-15 2:33 PM
>À : Fernandez Edgar; galaxy-...@bx.psu.edu
>Objet : Re: [galaxy-dev] FASTQ Groomer tool
>
> 
>
>Hi Edgar,
>you can try to restart Galaxy (both web and handler processes) and re-run the 
>tool.
>
>Cheers,
>Nicola
>
>On 05/11/15 19:18, Fernandez Edgar wrote:
>
>Hello again,
>
> 
>
>I installed today the tool : fastq_all_to_sanger
>
>I get the same SQL error with that one too.
>
>Any ideas guys?
>
> 
>
>Thank you!!!
>
> 
>
>Cordialement / Regards, 
>
>Edgar Fernandez
>
> 
>
>De : Fernandez Edgar 
>Envoyé : November-04-15 8:58 AM
>À : 'galaxy-...@bx.psu.edu'
>Objet : [galaxy-dev] FASTQ Groomer tool 
>
> 
>
>Hello gents,
>
> 
>
>I just installed "FASTQ Groomer tool" for the teachers to try it out and I’ve 
>been getting the following error than I do not understand:
>
> 
>
>galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: 
>/home/galaxy/galaxy-prod/database/job_working_directory/000/756
>
>galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 
>'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' 
>removed from tool config, unable to run job
>
>galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756
>
>Traceback (most recent call last):
>
>  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in 
>__monitor_step
>
>    job_state = self.__check_job_state( job )
>
>  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in 
>__check_job_state
>
>    state, job_destination = self.__verify_job_ready( job, job_wrapper )
>
>  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in 
>__verify_job_ready
>
>    job_wrapper.fail( e )
>
>  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in 
>fail
>
>    self.sa_session.flush()
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in 
>do
>
>    return getattr(self.registry(), name)(*args, **kwargs)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in 
>flush
>
>    self._flush(objects)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in 
>_flush
>
>    transaction.rollback(_capture_exception=True)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, 
>in __exit__
>
>    compat.reraise(exc_type, exc_value, exc_tb)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in 
>_flush
>
>    flush_context.execute()
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, 
>in execute
>
>    rec.execute(self)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, 
>in execute
>
>    uow
>
> File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, 
>in save_obj
>
>    mapper, table, update)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, 
>in _emit_update_statements
>
>    execute(statement, multiparams)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in 
>execute
>
>    return meth(self, multiparams, params)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in 
>_execute_on_connection
>
>    return connection._execute_clauseelement(self, multiparams, params)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in 
>_execute_clauseelement
>
>    compiled_sql, distilled_params
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in 
>_execute_context
>
>    context)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in 
>_handle_dbapi_exception
>
>    exc_info
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in 
>raise_from_cause
>
>    reraise(type(exception), exception, tb=exc_tb)
>
>  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", 

[galaxy-dev] Galaxy Url for Fasta and Bed index files

[Asma Riyaz]

Hello,

What is an appropriate galaxy URL to use to obtain bed and fasta index
files? I have tried below:

myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]_name=fasta.fai
{for fasta index}

and

myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]_name=bed.idx
{for bed index}

While looking through metadata for both bed and fasta file at:

myGalaxy.org:port/api/histories/[history_id]/contents/[api_id]

I realized that it lacks a meta_files list. Is there a way to populate this
list for bed and fasta files as well?

Example: For bam files this list populates as bam_index and hence I
use metadata_name=bam_index and an appropriate bai file downloads.

Thank you

Asma
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[galaxy-dev] Error in sh manage_db.sh -c ./config/galaxy.ini upgrade

[rbrown1422]

Dear Galaxy Dev Team,

We upgraded our Galaxy instance to the git repository from mercurial  old 
Galaxy-dist to Galaxy.  
When running the sh manage_db.sh -c ./config/galaxy.ini  upgrade   we get the 
following error.

Can you explain this error and more importantly how to correct the problem>

Thanks,
Bob

-bash-4.2$ sh manage_db.sh -c ./config/galaxy.ini upgradeTraceback (most recent 
call last):  File "./scripts/manage_db.py", line 33, in 
invoke_migrate_main()  File "./scripts/manage_db.py", line 30, in 
invoke_migrate_mainmain( repository=repo, url=db_url )  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py",
 line 209, in mainret = command_func(**kwargs)  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
 line 186, in upgradereturn _migrate(url, repository, version, 
upgrade=True, err=err, **opts)  File "", line 2, in _migrate  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py",
 line 160, in with_enginereturn f(*a, **kw)  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
 line 342, in _migrateschema = ControlledSchema(engine, repository)  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py",
 line 33, in __init__self.load()  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py",
 line 54, in loadexceptions.DatabaseNotControlledError(str(exc)), tb)  File 
"/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py",
 line 50, in loaddata = 
list(result)[0]migrate.exceptions.DatabaseNotControlledError: list index out of 
range-bash-4.2$ 

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Re: [galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

[Von Kuster, Greg]

Nicola, thanks a bunch!  Your eyes are phenomenal!

Greg

> On Nov 4, 2015, at 8:09 PM, Nicola Soranzo  wrote:
> 
> Hi Greg,
> in the inputs the param has name "input_gff", while in the test you are using 
> name "input".
> 
> Cheers, 
> Nicola 
> 
>  Von Kuster, Greg ha scritto 
> 
>> Hello Galaxy devs,
>> 
>> I’m developing a tool that uses a multi-select list to accept any number of 
>> input datasets.  The tool works fine when executing it within Galaxy, but 
>> when running it through planemo testing, it never passes, so I’m wondering 
>> if there are known issues with planemo testing tools that produce dataset 
>> collections.
>> 
>> I’ve spent some time adding debugging log statements into the Galaxy 
>> framework for planemo test runs, but haven’t uncovered anything obvious.  So 
>> if there are no known issues with planemo testing dataset_collections, I’m 
>> wondering if my tool config syntax is incorrect.
>> 
>> Does anyone see anything obvious?  Any insight is much appreciated!
>> 
>> Here is the command line.  Notice that I do not define any outputs since I 
>> am using a dataset collection.  Is this causing a problem for planemo?
>> 
>>   
>>   python $__tool_directory__/genetrack.py
>>   --input_format $input_format_cond.input_format
>>   #if str($input_format_cond.input_format) == "genetracktool":
>>   #for $i in $input_format_cond.input_genetracktool:
>>--input "${i}" "${i.hid}" "${i.name}"
>>   #end for
>>   #elif str($input_format_cond.input_format) == "gff":
>>   #for $i in $input_format_cond.input_gff:
>>--input "${i}" "${i.hid}" "${i.name}"
>>   #end for
>>   #end if
>>   --sigma $sigma
>>   --exclusion $exclusion
>>   --up_width $up_width
>>   --down_width $down_width
>>   --filter $filter
>>   --chromosome $chromosome
>>   --chunk_size $chunk_size
>>   --output_format $output_format
>>   
>> 
>> The input  dataset parameter looks like this:
>> 
>> > label="Predict peaks on" />
>> 
>> The tool produces a list of outputs, so I’ve defined a collection like this:
>> 
>>   
>>   
>>   > directory="output" ext="gff" visible="false" />
>>   
>>   
>> 
>> I’m using planemo, version 0.19.0.
>> 
>> Here is one of the tools’ functional test definitions.
>> 
>>   
>>   > ftype="gff" />
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   
>>   > ftype="gff" />
>>   
>>   
>> 
>> Here is the log from running the test with planemo.
>> 
>> Genetrack ( genetrack ) > Test-3 ... 
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,292 
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session 
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET 
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session 
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST 
>> /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST 
>> /api/histories HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST 
>> /api/tools HTTP/1.1" 400 None
>> ERROR
>> 
>> ==
>> ERROR: Genetrack ( genetrack ) > Test-1
>> --
>> Traceback (most recent call last):
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
>> line 289, in test_tool
>>   self.do_it( td )
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
>> line 58, in do_it
>>   raise e
>> RunToolException: Error creating a job for these tool inputs - Unknown error 
>> occurred while processing request.
>>  >> begin captured logging << 
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>> (1): localhost
>> galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
>> api key
>> requests.packages.urllib3.connectionpool: DEBUG: "GET 
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>> (1): localhost
>>