Re: [galaxy-dev] InvalidRequestError: kombu.transport.sqlalchemy.Queue

[Dannon Baker]

Hi Asma,

This is a known issue I'm still working on a permanent fix for.  For right
now, you can simply restart the process and it'll hopefully work fine --
we'll have a much better fix out soon.

-Dannon


On Thu, Apr 23, 2015 at 2:12 PM Asma Riyaz  wrote:

> Hi,
>
> I am receiving this traceback when I do restart Apache and not sure what
> to make of it:
>
> Exception in thread WorkflowRequestMonitor.monitor_thread:
>
> Traceback (most recent call last):
>
>   File
> "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py",
> line 530, in __bootstrap_inner
>
> self.run()
>
>   File
> "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py",
> line 483, in run
>
> self.__target(*self.__args, **self.__kwargs)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py",
> line 158, in __monitor
>
> self.__schedule( workflow_scheduler_id, workflow_scheduler )
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py",
> line 162, in __schedule
>
> invocation_ids = self.__active_invocation_ids( workflow_scheduler_id )
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py",
> line 191, in __active_invocation_ids
>
> handler=handler,
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/model/__init__.py",
> line 3254, in poll_active_workflow_ids
>
> WorkflowInvocation
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/scoping.py",
> line 150, in do
>
> return getattr(self.registry(), name)(*args, **kwargs)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py",
> line 1165, in query
>
> return self._query_cls(entities, self, **kwargs)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
> line 108, in __init__
>
> self._set_entities(entities)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
> line 118, in _set_entities
>
> self._set_entity_selectables(self._entities)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
> line 151, in _set_entity_selectables
>
> ent.setup_entity(*d[entity])
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py",
> line 3036, in setup_entity
>
> self._with_polymorphic = ext_info.with_polymorphic_mappers
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py",
> line 725, in __get__
>
> obj.__dict__[self.__name__] = result = self.fget(obj)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py",
> line 1877, in _with_polymorphic_mappers
>
> configure_mappers()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py",
> line 2589, in configure_mappers
>
> mapper._post_configure_properties()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py",
> line 1694, in _post_configure_properties
>
> prop.init()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/interfaces.py",
> line 144, in init
>
> self.do_init()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py",
> line 1549, in do_init
>
> self._process_dependent_arguments()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py",
> line 1605, in _process_dependent_arguments
>
> self.target = self.mapper.mapped_table
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py",
> line 725, in __get__
>
> obj.__dict__[self.__name__] = result = self.fget(obj)
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py",
> line 1522, in mapper
>
> argument = self.argument()
>
>   File
> "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/ext/declarative/clsregistry.py",
> line 283, in __call__
>
> (self.prop.parent, self.arg, n.args[0], self.cls)
>
> InvalidRequestError: When initializing mapper Mapper|Queue|kombu_queue,
> expression 'Message'

[galaxy-dev] error in Galaxy (lefse)

[Borruso Luigimaria]

Dear Galaxy-project staff,

in the last two weeks, I have tried several time to use Lefse but it seems to 
have some problem. I always get the following message: Internal Server Error 
Galaxy was unable to successfully complete your request. An error occurred. 
This may be an intermittent problem due to load or other unpredictable factors, 
reloading the page may address the problem. The error has been logged to our 
team.

Thanks a lot


Luigi Borruso, PhD
Environmental Microbiology

Faculty of Science & Technology
Building K, Office 1.05
Free University of Bozen/Bolzano
Piazza Università 5
I-39100 Bozen/Bolzano
Italy

Tel. +39 0471 017610
E-mail: luigimaria.borr...@unibz.it
Website: www.unibz.it/sciencetechnology


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[galaxy-dev] SSL/LDAP configuration for CloudMan/Galaxy

[David Kovalic]

Hi,


We are interested in running CloudMan/Galaxy with SSL and LDAP. After
searching around on the internet it seems like this is achievable and
probably not too difficult, but there is no current complete “cookbook
recipe” for doing so, so I thought it best to ask questions before I go
ahead and break stuff :)


 As I understand:

· ngnix needs to have the LDAP module added, as the standard CM
ngnix build doesn’t include this

· ngnix needs to have a custom ngnix.conf file which specifies the
use of SSL and LDAP

· Galaxy need to have a custom configuration universe_wsgi.ini for
LDAP use


   By searching online I can’t clearly figure out:

· How to recompile (and persist across CM cluster
termination/restart) a new version of ngnix

· The best way to maintain and specify a custom ngnix.conf. Is it
possible to do this by placing the custom ngnix.conf in the cluster S3
bucket and adding a configuration line specifying its URL (e.g.
"nginx_conf_contents: https://s3.amazonaws.com/[cm bucket ID]/ngnix.conf")
in persistent_data.yaml file in the CM S3 bucket?

· Where do I make the modifications such that the changes to
universe_wsgi.ini persist across CM cluster termination/restart?

   It would be great to get some experienced insight on how best to
complete this configuration, and have it persist.


Any guidance would be greatly appreciated. Thanks,


David Kovalic
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[galaxy-dev] README.rst missing on Tool Shed display?

[Peter Cock]

Hi all,

I don't see tool README files on the main view of a repository
any more. Is this a recent regression?

e.g. https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
and https://testtoolshed.g2.bx.psu.edu/view/bgruening/deeptools
should show the readme.rst file

e.g. https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
and https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
should show the README.rst file

This might be specific to restructured-text markup - I'd have to trawl
the ToolShed looking for a plain text README file to check that.

Regards,

Peter
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Re: [galaxy-dev] History panel error

[Dannon Baker]

Hi Jose,

Can you review (and share, maybe) the relevant part of the logs from when
you attempt to execute a job?  It'd be worth it, if you still have the
logs, to know what the "Internal Server Error" indicated in your first
message was, as well.

-Dannon

On Fri, Apr 24, 2015 at 11:00 AM Jose Juan Almagro Armenteros <
jjalma...@gmail.com> wrote:

> Hi again,
>
> Now it is working, I just went back to the previous version and updated it
> again. All is okay except that the job table in the postgresql database is
> empty and is not being updated with new jobs (the problem is only with this
> table). I run manage_db.sh upgrade but nothing happened.
>
> Do you know what could be causing this?
>
> Thank you again!
>
> Best regards,
>
> Jose
>
> 2015-04-24 14:22 GMT+02:00 Jose Juan Almagro Armenteros <
> jjalma...@gmail.com>:
>
>> Hello all,
>>
>> I have updated my Galaxy distribution today to the latest version 15.03
>> and the history panel is not being shown. The history seems to be there but
>> Galaxy can't display the datasets.  Even if I create a new history and I
>> run a tool the dataset is not shown. It is just displayed an error which
>> says: "An error occurred while getting updates from the server..." and the
>> details shows this:
>>
>> {
>>   "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like 
>> Gecko) Chrome/37.0.2062.120 Safari/537.36",
>>   "url": 
>> "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9f/contents";,
>>   "data": "",
>>   "options": {
>> "data": {},
>> "silent": true,
>> "parse": true,
>> "emulateHTTP": false,
>> "emulateJSON": false
>>   },
>>   "xhr": {
>> "readyState": 4,
>> "responseText": "{\"err_msg\": \"Uncaught exception in exposed API 
>> method:\", \"err_code\": 0}",
>> "responseJSON": {
>>   "err_msg": "Uncaught exception in exposed API method:",
>>   "err_code": 0
>> },
>> "status": 500,
>> "statusText": "Internal Server Error",
>> "responseHeaders": {
>>   "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r",
>>   "cache-control": "max-age=0,no-cache,no-store\r",
>>   "Transfer-Encoding": "chunked\r",
>>   "Server": "PasteWSGIServer/0.5 Python/2.7.3\r",
>>   "Connection": "close\r",
>>   "x-frame-options": "SAMEORIGIN\r",
>>   "content-type": "application/json\r"
>> }
>>   },
>>   "source": [],
>>   "user": {
>> "username": "jose",
>> "quota_percent": 0,
>> "total_disk_usage": 101352147,
>> "nice_total_disk_usage": "96.7 MB",
>> "email": "jjalma...@gmail.com",
>> "is_admin": true,
>> "tags_used": [],
>> "model_class": "User",
>> "id": "72ad249754f05d26"
>>   }
>> }
>>
>> Do you have any idea what could go wrong?
>>
>> Thank you and best regards,
>>
>> Jose
>>
>
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Re: [galaxy-dev] History panel error

[Jose Juan Almagro Armenteros]

Hi again,

Now it is working, I just went back to the previous version and updated it
again. All is okay except that the job table in the postgresql database is
empty and is not being updated with new jobs (the problem is only with this
table). I run manage_db.sh upgrade but nothing happened.

Do you know what could be causing this?

Thank you again!

Best regards,

Jose

2015-04-24 14:22 GMT+02:00 Jose Juan Almagro Armenteros :

> Hello all,
>
> I have updated my Galaxy distribution today to the latest version 15.03
> and the history panel is not being shown. The history seems to be there but
> Galaxy can't display the datasets.  Even if I create a new history and I
> run a tool the dataset is not shown. It is just displayed an error which
> says: "An error occurred while getting updates from the server..." and the
> details shows this:
>
> {
>   "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like 
> Gecko) Chrome/37.0.2062.120 Safari/537.36",
>   "url": 
> "http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9f/contents";,
>   "data": "",
>   "options": {
> "data": {},
> "silent": true,
> "parse": true,
> "emulateHTTP": false,
> "emulateJSON": false
>   },
>   "xhr": {
> "readyState": 4,
> "responseText": "{\"err_msg\": \"Uncaught exception in exposed API 
> method:\", \"err_code\": 0}",
> "responseJSON": {
>   "err_msg": "Uncaught exception in exposed API method:",
>   "err_code": 0
> },
> "status": 500,
> "statusText": "Internal Server Error",
> "responseHeaders": {
>   "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r",
>   "cache-control": "max-age=0,no-cache,no-store\r",
>   "Transfer-Encoding": "chunked\r",
>   "Server": "PasteWSGIServer/0.5 Python/2.7.3\r",
>   "Connection": "close\r",
>   "x-frame-options": "SAMEORIGIN\r",
>   "content-type": "application/json\r"
> }
>   },
>   "source": [],
>   "user": {
> "username": "jose",
> "quota_percent": 0,
> "total_disk_usage": 101352147,
> "nice_total_disk_usage": "96.7 MB",
> "email": "jjalma...@gmail.com",
> "is_admin": true,
> "tags_used": [],
> "model_class": "User",
> "id": "72ad249754f05d26"
>   }
> }
>
> Do you have any idea what could go wrong?
>
> Thank you and best regards,
>
> Jose
>
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Re: [galaxy-dev] Galaxy for Natural Language Processing

[Bjoern Gruening]

On 24.04.2015 03:18, Keith Suderman wrote:

Hi Björn,

On Apr 22, 2015, at 8:00 AM, Björn Grüning > wrote:



Do you have a beer preference?


Outing: I'm one of the rare Germans that do not drink alcohol ;)


That must be awkward ;)


:)




This can be done via the ToolShed. I assume your custom command
interpreter is not different than python or perl as interpreter?


One difference is that my interpreter is a Java program. I likely 
should have mentioned that little detail... anyone wanting to install 
our tools would need my interpreter AND Java 1.7+ on their server. 
 Hopefully that is not an insurmountable problem.


In Galaxy we advertise people to have a JRE around if they use the TS. 
Currently, the TS is not able it install Java. I was not able to compile 
java by my own :(

https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList

So this is ok!

However, does the bioinformatics community really want a bunch of NLP 
tools in their tool shed?


Yes, Yes, Yes!

The editor also allows me to select output formats that have no 
converters defined,
so either I am still missing something or the workflow editor does 
not do what I want.  I can convert formats through the "Edit 
attributes" menu,
so Galaxy knows about my converters and how to invoke them, just not 
in the workflow editor.


Ok, I think I understood. Not sure if this is the best way but put your
converters into the toolbox.


By the "toolbox" do you mean adding my converters to the tool_conf.xml 
file so they are available on the Tools menu?  I have done that and I 
can add the converters to a workflow manually. I was just hoping the 
workflow editor could detect when it could perform the conversion and 
insert the converters as needed; it seems this is not possible.


Maybe someone else can jump in here, I do not see why this shouldn't be 
possible? Maybe this is just an UI issue?!


Do you have more pointers to tools that use the attached metadata? 
 In particular tools that set metadata that is consumed by 
subsequent tools.


The sqlite datatype should be a good example. Keep in mind, we can not
set metadata from inside a tool.
Imho this is not possible, yet, but a
common requested feature. But you can "calculate" such metadata inside
your datatype definition and set it implicitly after your tool is 
finished.


Setting the metadata in the tool wrapper is fine, and after grepping 
through some of the other wrappers I think I need something like:


  
  


True


  

  
  

metadata.tokens is not None


  

That is, the input validator simply checks if some value has been set 
in the metadata, and the output sets a value in the metadata.  The 
above does not work, but at least Galaxy stopped complaining about the 
tool XML with this.  However, the documentation for  
 and  does not match up with what existing wrappers 
(in the dev branch) are doing so I am having problems with the exact 
syntax.


Can you try: 

You can also filter your inputs in the speech tagger:

  type="add_value" value="True" /> 





Do you have pointers to any documentation on data collections?  My 
searches haven't turned up much but tantalizing references [1],
and my experiments trying to return a data collection from a tool 
have been unsuccessful.


https://wiki.galaxyproject.org/Histories?highlight=%28collection%29#Dataset_Collections

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax ->
data_collection

And have a look at:
https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools


Success!  I was running the code from master, so I suspect that was 
part of my problem.


Nice!


However, my browser is still complaining about long running scripts.


Can you put this in a different thread?


A script on this page may be busy, or it may have stopped
responding. You can stop the script now, open the script in the
debugger, or let the script continue.

Script:
http://localhost:8000/static/s…/jquery/jquery.js?v=1429811186:2




I accidentally left visible="true" when creating the dataset 
collection and ended up with +1500 items in my history; the above 
message kept popping up while the workflow was running (at least until 
I selected "Don't show this again").  Deleting +1500 datasets from the 
history is also very slow, but that is a different issue. On the 
bright side, at least I had +1500 items in the history to delete.


+1500 different elements is a lot for a history, for usability we should 
try to use collections here. No one wants to deal with such an mount of 
history objects :)




I have also been trying John Chiltons blend4j and managed to 
populate a data library, and this is almost what I want,
but I would like a tool that can be included in a workflow as the 
data from the library may not necessarily be the first step.
I have no p

Re: [galaxy-dev] question about splitting bams

[Roberto Alonso CIPF]

Hello,

I have been reading those different threads  and I have some doubts that
you maybe can clarify me. In the thread you said: "ability to write tools
that split up a single input into a collection. ", I think this is focused
for workflows, but in any case, could we use this to split bams?
Another comment is the next:

"These common pipelines where you split up a BAM files, run a bunch of
steps, and then merge the results will be executable in the near
future (though 15.03 won't have workflow editor support for it - I
will try to get to this by the following release - and you can
manually build up workflows to do this - "

As I was trying to write something that will do exactly this and I guess
there is someone working on this, do you think is it worth to continue
doing this or just switch to another thing? would you know the road-map of
this feature?

Thanks a lot,

Roberto

On 23 April 2015 at 20:09, John Chilton  wrote:

> I am a pragmatist - I have no problem just splitting the inputs and
> skipping the metadata files. I would just convert the error into an
> log.info() and warn that the tool cannot use metadata files. If the
> underlying tool needs an index it can recreate it instead I think. One
> can imagine a more intricate solution that would recreate metadata
> files as needed - but that would be a lot of work I think.
>
> Does that make sense?
>
> About BB PR 175 there were some recent discussions about that approach
> - I would check out
> http://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html
> .
>
> -John
>
> On Thu, Apr 23, 2015 at 11:55 AM, Roberto Alonso CIPF 
> wrote:
> > Hello,
> > I ma trying ti write some code in order to give the possibility of
> > parallelize some tasks. Now, I was with the problem of splitting a bam in
> > some parts, for this I create this simple tool
> >
> >  > merge_outputs="output" split_inputs="input" >
> >
> >   
> > java -jar
> > /home/ralonso/software/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T
> > UnifiedGenotyper -R /home/ralonso/BiB/Galaxy/data/chr_19_hg19_ucsc.fa -I
> > $input -o $output 2> /dev/null;
> >
> >   
> >   
> > 
> >   
> >   
> >   
> >   
> >
> > But I have one problem, when I execute the tool it goes through this
> part of
> > code (I am working in dev branch):
> >
> > $galaxy/lib/galaxy/jobs/splitters/multi.py, line 75:
> >
> > for input in parent_job.input_datasets:
> > if input.name in split_inputs:
> > this_input_files =
> > job_wrapper.get_input_dataset_fnames(input.dataset)
> > if len(this_input_files) > 1:
> > log_error = "The input '%s' is composed of multiple
> files -
> > splitting is not allowed" % str(input.name)
> > log.error(log_error)
> > raise Exception(log_error)
> > input_datasets.append(input.dataset)
> >
> > So, it is raising the exception because this_input_files=2, concretely:
> > ['/home/ralonso/galaxy/database/files/000/dataset_171.dat',
> >
> '/home/ralonso/galaxy/database/files/_metadata_files/000/metadata_13.dat'],
> > I guess that:
> > dataset_171.dat: It is the bam file.
> > metadata_13.dat: It is the bai file.
> >
> > So, Galaxy can't move on and I don't know which would be the best
> solution.
> > Maybe change the if to check only non-metadata files? I think I should
> use
> > both files in order to create the bam sub-files, but this would be inside
> > the Bam class, under binary.py file.
> > Could you please guide me before I mess things up?
> >
> > Thanks so much
> > --
> > Roberto Alonso
> > Functional Genomics Unit
> > Bioinformatics and Genomics Department
> > Prince Felipe Research Center (CIPF)
> > C./Eduardo Primo Yúfera (Científic), nº 3
> > (junto Oceanografico)
> > 46012 Valencia, Spain
> > Tel: +34 963289680 Ext. 1021
> > Fax: +34 963289574
> > E-Mail: ralo...@cipf.es
> >
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-- 
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es
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Re: [galaxy-dev] Job submission failed

[John Chilton]

I am pretty stumped by this - my next actions would be to upgrade to
the newest latest_15.03 in case this has been fixed.

If that doesn't fix it I might look at your proxy configuration - is
there a proxy server sitting in front of Galaxy? It looks like upload
works on this server and I believe that is using the same endpoint
POST /api/tools. I don't know why upload would work but all other
tools fail - but one possibility is the proxy is blocking the request
if it doesn't look like an upload.

-John

On Tue, Apr 21, 2015 at 10:11 PM, Vipin TS  wrote:
> Hi John,
>
> I am seeing an error in browser console when click on a tool link:
> POST https://galaxy.cbio.mskcc.org/api/tools 403 (Forbidden)
>
> "
> 
> 403 Forbidden
> 
> Forbidden
> You don't have permission to access /api/tools
> on this server.
> 
>
> which points to the tool-jobs.js line #65, which is the error part of the
> Utils.request  function.
> Something related with authentication?
>
> Vipin
>
> On Tue, Apr 21, 2015 at 9:05 AM, John Chilton  wrote:
>>
>> Another question is are there any logs indicating issues on the server
>> side and can you open your web console and let us know if there are
>> any errors reported there on the client side (e.g.
>> https://developer.mozilla.org/en-US/docs/Tools/Web_Console).
>>
>> -John
>>
>> On Tue, Apr 21, 2015 at 3:45 AM, Hans-Rudolf Hotz  wrote:
>> > Hi Vipin
>> >
>> > Is this a new problem you encounter since you have done the upgrade to
>> > "latest_15.03"? If so, did you experience any troubles during the
>> > database
>> > schema upgrade to '128'?
>> >
>> >
>> > Regards, Hans-Rudolf
>> >
>> >
>> > On 04/20/2015 08:44 PM, Vipin TS wrote:
>> >>
>> >> Hi dev-team,
>> >>
>> >>
>> >> I am experiencing an issue with my production instance in dispatching
>> >> the jobs. When I click on execute button, each tool page shows the
>> >> popup
>> >> error message as here:
>> >> Inline image 1
>> >> I am not sure what is happening, not getting any single line of error
>> >> message in log file.
>> >>
>> >> Here is the version I am using:
>> >> changeset:   17051:28113212
>> >> branch:  stable
>> >> date:Mon Mar 16 22:38:27 2015 -0400
>> >> summary: Update tag latest_15.03 for changeset 9f40ff3e3fe1
>> >>
>> >> any suggestions, Thank you!
>> >>
>> >> Vipin | Rätsch Lab
>> >>
>> >>
>> >> ___
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>> >>
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>
>
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[galaxy-dev] History panel error

[Jose Juan Almagro Armenteros]

Hello all,

I have updated my Galaxy distribution today to the latest version 15.03 and
the history panel is not being shown. The history seems to be there but
Galaxy can't display the datasets.  Even if I create a new history and I
run a tool the dataset is not shown. It is just displayed an error which
says: "An error occurred while getting updates from the server..." and the
details shows this:

{
  "agent": "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML,
like Gecko) Chrome/37.0.2062.120 Safari/537.36",
  "url": 
"http://galaxy.bric.ku.dk/history/view_multipl/api/histories/782c6cc7ec4cfd9f/contents";,
  "data": "",
  "options": {
"data": {},
"silent": true,
"parse": true,
"emulateHTTP": false,
"emulateJSON": false
  },
  "xhr": {
"readyState": 4,
"responseText": "{\"err_msg\": \"Uncaught exception in exposed API
method:\", \"err_code\": 0}",
"responseJSON": {
  "err_msg": "Uncaught exception in exposed API method:",
  "err_code": 0
},
"status": 500,
"statusText": "Internal Server Error",
"responseHeaders": {
  "Date": "Fri, 24 Apr 2015 12:09:40 GMT\r",
  "cache-control": "max-age=0,no-cache,no-store\r",
  "Transfer-Encoding": "chunked\r",
  "Server": "PasteWSGIServer/0.5 Python/2.7.3\r",
  "Connection": "close\r",
  "x-frame-options": "SAMEORIGIN\r",
  "content-type": "application/json\r"
}
  },
  "source": [],
  "user": {
"username": "jose",
"quota_percent": 0,
"total_disk_usage": 101352147,
"nice_total_disk_usage": "96.7 MB",
"email": "jjalma...@gmail.com",
"is_admin": true,
"tags_used": [],
"model_class": "User",
"id": "72ad249754f05d26"
  }
}

Do you have any idea what could go wrong?

Thank you and best regards,

Jose
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Re: [galaxy-dev] Galaxy for Natural Language Processing

[Nicola Soranzo]

Il 24.04.2015 03:18 Keith Suderman ha scritto:

This can be done via the ToolShed. I assume your custom command
interpreter is not different than python or perl as interpreter?


One difference is that my interpreter is a Java program. I likely 
should
have mentioned that little detail... anyone wanting to install our 
tools
would need my interpreter AND Java 1.7+ on their server. Hopefully 
that

is not an insurmountable problem.
However, does the bioinformatics community really want a bunch of NLP
tools in their tool shed?


Sorry to jump in here, I'd only like to confirm you that we would 
appreciate to have your NLP tools in the ToolShed, that would help us 
prove the fact that Galaxy is a useful platform also in other scientific 
fields.


Cheers,
Nicola


Connetti gratis il mondo con la nuova indoona:  hai la chat, le 
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Re: [galaxy-dev] Data Libraries

[Nicola Soranzo]

  You may just use a different folder for each project inside a
"Sequencing" library. Would that work?

Nicola

Il 24.04.2015 13:10 Ryan
G ha scritto: 

> This could work. In the long run though, after
sequencing for a project, we'd like them people in the sequencing lab to
be able to add the data to Galaxy in project specific libraries, without
having an admin create a library for them. 
> 
> On Thu, Apr 23, 2015 at
4:56 PM, Martin Čech wrote:
> 
>> Hello Ryan, 
>> it is currently not
possible to give users rights to create data libraries. However you can
create the libraries for them and give them rights to create and manage
subfolders (doing the same things but one level below). 
>> Would that
address your goal? 
>> Martin
>> 
>> On Thu, Apr 23, 2015 at 4:33 PM
Ryan G wrote:
>> 
>>> Hi all - We are trying to use Galaxy as a
mechanism for our sequencing lab to create data libraries for data they
generate. I noticed in the docs, only Admins are able to create data
libraries. Is there a way to change this? I'd like to give specific
users in our group this ability without giving them admin rights.
>>>

>>> Ryan
>>> 
>>>
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[1]
>>> 
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at:
>>> http://galaxyproject.org/search/mailinglists/ [2]
 



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Re: [galaxy-dev] Data Libraries

[Ryan G]

This could work.  In the long run though, after sequencing for a project,
we'd like them people in the sequencing lab to be able to add the data to
Galaxy in project specific libraries, without having an admin create a
library for them.

On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech  wrote:

> Hello Ryan,
>
> it is currently not possible to give users rights to create data
> libraries. However you can create the libraries for them and give them
> rights to create and manage subfolders (doing the same things but one level
> below).
> Would that address your goal?
>
> Martin
>
> On Thu, Apr 23, 2015 at 4:33 PM Ryan G 
> wrote:
>
>> Hi all - We are trying to use Galaxy as a mechanism for our sequencing
>> lab to create data libraries for data they generate.  I noticed in the
>> docs, only Admins are able to create data libraries.  Is there a way to
>> change this?  I'd like to give specific users in our group this ability
>> without giving them admin rights.
>>
>> Ryan
>>
>> ___
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>
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