Re: [galaxy-dev] Mira-Assembler: DOESN'T WORK ON GALAXY

[Marija Atanaskovic]

Mira doesn’t work on Galaxy. This is the log message I receive.
Tool: Assemble with MIRA v3.4
Name:   MIRA log
Created:Fri Aug 22 00:24:38 2014 (UTC)
Filesize:   0 bytes
Dbkey:  ?
Format: txt
Galaxy Tool Version:0.0.10
Tool Version:   None
Tool Standard Output:   
stdout
Tool Standard Error:
stderr
Tool Exit Code: None
API ID: d5f55b83db1f410a
Full Path:  /mnt/galaxy/files/000/dataset_326.dat

Input Parameter Value   Note for rerun
Assembly method De novo
Assembly type   Genome
Assembly quality grade  Accurate
Backbones/reference chromosomes?false
Sanger/Capillary reads? false
454 reads?  false
Solexa/Illumina reads?  false
Ion Torrent reads?  true
Ion Torrent reads file  10: 
R_2011_10_19_14_30_56_user_SN1-36_Auto_SN1-36_38.fastq
Inheritance Chain
MIRA log

Also I can’t install Mira 4. This is the message I receive. Any suggestions.

Thanks.

Marija Tauschek

--
Dr Marija Tauschek/Atanaskovic
Robins-Browne Lab
Dept Microbiology & Immunology,
The University of Melbourne,
at the Peter Doherty Institute for Infection and Immunity,
Victoria 3010, Australia
Tel: +61 3 8344 9927
Email: ma...@unimelb.edu.au
Internal Server Error
Galaxy was unable to successfully complete your request

URL: 
http://130.56.251.91/admin_toolshed/prepare_for_install?tool_shed_url=https://testtoolshed.g2.bx.psu.edu/&repository_ids=4dd4d179ddfb3445&changeset_revisions=aeb3e35f8236
Module galaxy.web.framework.middleware.error:149 in __call__
>>  
>> 
>>  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
>>  
>> 
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  
>> 
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>>  
>> 
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>>  
>> 
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:369 in decorator
>>  
>> 
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:983 in 
prepare_for_install
>>  
>> 
>>  includes_tool_dependencies )
Module tool_shed.util.common_install_util:97 in get_dependencies_for_repository
>>  
>> 
>>  repository = suc.get_repository_for_dependency_relationship( trans.app, 
>> tool_shed_url, name, repository_owner, changeset_revision )
Module tool_shed.util.shed_util_common:1036 in 
get_repository_for_dependency_relationship
>>  
>> 
>>  ( name, owner, changeset_revision ) )
Module tool_shed.util.shed_util_common:1867 in url_join
>>  
>> 
>>  parts.append( arg.strip( '/' ) )
AttributeError: 'NoneType' object has no attribute 'strip'
extra 
data

full 
traceback

text 
version

[galaxy-dev] Problems downloading files via bioblend

[Brad Zeitner]

I have a python script that I use to download the qc data generated in one of 
the steps in a workflow.
It used to work on a previous install of galaxy - but we've gone through and 
updated our Galaxy install so that it's now running on a new file system - and 
when I try and use the bioblend api to download the dataset the request for the 
file gets redirected to the login page.

The call to download it is -
dm = gi.datasets.download_dataset(qcf.get("id"), outfile, False )
Where qcf is the history step
This calls the following url:/datasets/4fa2da3cf0e735a4/display?to_ext=html

If I visit the url in a browser that's not in a session, it behaves the same 
way - but works correctly when I am logged in.
How can I access this using the api key?  When I add the parameters 
key=${myKey}  it still fails.

Thanks,
-Brad Zeitner


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Re: [galaxy-dev] bioblend run_workflow (no_wait?)

[Dannon Baker]

So, see the commentary on the bioblend issue you added as well, but in
short -- while you should currently expect to wait while the entire
workflow was queued, bioblend *should not* be blocking waiting for all jobs
to complete and that sounds like a bioblend bug if it is.  That's what the
'wait' param is for after all.


On Thu, Aug 21, 2014 at 5:27 PM, Evan Bollig  wrote:

> Thanks Dannon. Looking forward to the resolution. We've got some long
> workflows (100+ steps) that take days to compute. It takes about 2
> minutes to finish queuing tasks, and then I found that they continue
> to execute even if I interrupt the bioblend thread. I'll add a
> signal.alarm interrupt to kill the bioblend thread and continue manual
> monitoring.
>
> -E
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.edu
>
>
> On Thu, Aug 21, 2014 at 4:20 PM, Dannon Baker 
> wrote:
> > There is no reason workflow invocation *has* to be synchronous, but
> that's
> > how galaxy works right now as, mostly, a historical artifact.  Workflow
> > scheduling happens inside the web request, and other than bioblend
> issuing
> > the request in another thread there won't be an implementation w/
> no_wait.
> > This is definitely suboptimal, and backgrounded (among other
> enhancements to
> > scheduling) workflow invocation is something we're working on right now,
> and
> > it's a high priority.
> >
> >
> > On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig  wrote:
> >>
> >> I'm using bioblend to launch a workflow, but i find that the
> >> gi.workflows.run_workflow() command does not provide an option for
> >> no_wait.
> >>
> >> Can anyone provide justification for why this needs to be synchronous?
> >>
> >> -Evan Bollig
> >> Research Associate | Application Developer | User Support Consultant
> >> Minnesota Supercomputing Institute
> >> 599 Walter Library
> >> 612 624 1447
> >> e...@msi.umn.edu
> >> boll0...@umn.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/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>   http://galaxyproject.org/search/mailinglists/
> >
> >
>
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Re: [galaxy-dev] bioblend run_workflow (no_wait?)

[Evan Bollig]

Thanks Dannon. Looking forward to the resolution. We've got some long
workflows (100+ steps) that take days to compute. It takes about 2
minutes to finish queuing tasks, and then I found that they continue
to execute even if I interrupt the bioblend thread. I'll add a
signal.alarm interrupt to kill the bioblend thread and continue manual
monitoring.

-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu


On Thu, Aug 21, 2014 at 4:20 PM, Dannon Baker  wrote:
> There is no reason workflow invocation *has* to be synchronous, but that's
> how galaxy works right now as, mostly, a historical artifact.  Workflow
> scheduling happens inside the web request, and other than bioblend issuing
> the request in another thread there won't be an implementation w/ no_wait.
> This is definitely suboptimal, and backgrounded (among other enhancements to
> scheduling) workflow invocation is something we're working on right now, and
> it's a high priority.
>
>
> On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig  wrote:
>>
>> I'm using bioblend to launch a workflow, but i find that the
>> gi.workflows.run_workflow() command does not provide an option for
>> no_wait.
>>
>> Can anyone provide justification for why this needs to be synchronous?
>>
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> e...@msi.umn.edu
>> boll0...@umn.edu
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
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Re: [galaxy-dev] bioblend run_workflow (no_wait?)

[Dannon Baker]

There is no reason workflow invocation *has* to be synchronous, but that's
how galaxy works right now as, mostly, a historical artifact.  Workflow
scheduling happens inside the web request, and other than bioblend issuing
the request in another thread there won't be an implementation w/ no_wait.
 This is definitely suboptimal, and backgrounded (among other enhancements
to scheduling) workflow invocation is something we're working on right now,
and it's a high priority.


On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig  wrote:

> I'm using bioblend to launch a workflow, but i find that the
> gi.workflows.run_workflow() command does not provide an option for
> no_wait.
>
> Can anyone provide justification for why this needs to be synchronous?
>
> -Evan Bollig
> Research Associate | Application Developer | User Support Consultant
> Minnesota Supercomputing Institute
> 599 Walter Library
> 612 624 1447
> e...@msi.umn.edu
> boll0...@umn.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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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[galaxy-dev] bioblend run_workflow (no_wait?)

[Evan Bollig]

I'm using bioblend to launch a workflow, but i find that the
gi.workflows.run_workflow() command does not provide an option for
no_wait.

Can anyone provide justification for why this needs to be synchronous?

-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
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[galaxy-dev] Database integrity error when installing new tools from toolshed

[Michael Ta]

Hi,

I updated a local Galaxy installation a while back and I followed the steps
listed on one of the wiki pages. The update included changes to the
database schema and I was careful to backup and restore it according to the
directions. However, when I try to install new tools from the tool shed or
update a tool to a new revision it does not complete successfully. The
following error appears in the log file.

File '/home/galaxy/galaxy-dist/lib/tool_shed/util/tool_util.py', line 761
in handle_tool_versions
context.flush()
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py',
   line 114 in do
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
   line 1718 in flush
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
   line 1789 in _flush
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p
  y', line 331 in execute
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.p
  y', line 475 in execute
 File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.
  py', line 64 in save_obj
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.
  py', line 558 in _emit_insert_statements
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
   line 1449 in execute
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
   line 1584 in _execute_clauseelement
 File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
   line 1698 in _execute_context
File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
   line 1691 in _execute_context
 File
'/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.p
  y', line 331 in do_execute
IntegrityError: (IntegrityError) duplicate key value violates unique
constraint "tool_version_association_pk   ey"
DETAIL:  Key (id)=(83) already exists.
'INSERT INTO tool_version_association (tool_id, parent_id) VALUES
(%(tool_id)s, %(parent_id)s) RETURNING to   ol_version_association.id'
{'parent_id': 440, 'tool_id': 439}

A few of the keys appear to be colliding with values already in the
database, did I miss something when I updated and restored the database
that is causing this?

Thanks,
-- 
Michael Ta
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Re: [galaxy-dev] How to build an application that uses a set of files?

[John Chilton]

Hmm... in that case I think you can just create a multiple input data parameter.



You can iterate through the files in your  tag and pass them
to your merge.py file:

merge.py #for $input in $inputs# $input
#end for# ...


This works unless you literally need 9 files - this input type doesn't
support min/max right now. (There is a Trello card that includes
adding such functionality if you want to vote on it
https://trello.com/c/lp5YmA1O).

I hope this helps - let me know if this is not quite right.

-John


On Thu, Aug 21, 2014 at 3:30 PM, George Weingart
 wrote:
> They are totally dynamic.
> Say all the files of tabular type that the User has at the moment.
>
>
> On Thu, Aug 21, 2014 at 12:28 PM, John Chilton  wrote:
>>
>> Are these 17 files fairly dynamic - i.e. are they going to depend on
>> previous steps in a history or user uploads - or are they literally
>> just 17 more or less fixed files associated with that tool and every
>> user should see roughly the same 17 options.
>>
>> -John
>>
>> On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
>>  wrote:
>> > Hello,
>> >
>> >
>> > I would like to get advice how to implement the following application
>> > into
>> > Galaxy:
>> >
>> >
>> > We have a set of say, 17 tabular files,   we would like to present them
>> > to
>> > the User and allow him to select a subset of them,  say 9.
>> >
>> > Once he selected these files we would like to invoke our program
>> > “merge.py”
>> > against the subset of 9 files the User selected whose result is an
>> > output of
>> > one file.
>> >
>> > How would the xml look?
>> >
>> >
>> > Thanks!
>> > George Weingart
>> >
>> >
>> >
>> > ___
>> > 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/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>
>

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Re: [galaxy-dev] How to build an application that uses a set of files?

[George Weingart]

They are totally dynamic.
Say all the files of tabular type that the User has at the moment.


On Thu, Aug 21, 2014 at 12:28 PM, John Chilton  wrote:

> Are these 17 files fairly dynamic - i.e. are they going to depend on
> previous steps in a history or user uploads - or are they literally
> just 17 more or less fixed files associated with that tool and every
> user should see roughly the same 17 options.
>
> -John
>
> On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
>  wrote:
> > Hello,
> >
> >
> > I would like to get advice how to implement the following application
> into
> > Galaxy:
> >
> >
> > We have a set of say, 17 tabular files,   we would like to present them
> to
> > the User and allow him to select a subset of them,  say 9.
> >
> > Once he selected these files we would like to invoke our program
> “merge.py”
> > against the subset of 9 files the User selected whose result is an
> output of
> > one file.
> >
> > How would the xml look?
> >
> >
> > Thanks!
> > George Weingart
> >
> >
> >
> > ___
> > 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/
> >
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>
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Re: [galaxy-dev] How to build an application that uses a set of files?

[John Chilton]

Are these 17 files fairly dynamic - i.e. are they going to depend on
previous steps in a history or user uploads - or are they literally
just 17 more or less fixed files associated with that tool and every
user should see roughly the same 17 options.

-John

On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
 wrote:
> Hello,
>
>
> I would like to get advice how to implement the following application into
> Galaxy:
>
>
> We have a set of say, 17 tabular files,   we would like to present them to
> the User and allow him to select a subset of them,  say 9.
>
> Once he selected these files we would like to invoke our program “merge.py”
> against the subset of 9 files the User selected whose result is an output of
> one file.
>
> How would the xml look?
>
>
> Thanks!
> George Weingart
>
>
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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[galaxy-dev] How to build an application that uses a set of files?

[George Weingart]

Hello,

I would like to get advice how to implement the following application into
Galaxy:

We have a set of say, 17 tabular files,   we would like to present them to
the User and allow him to select a subset of them,  say 9.

Once he selected these files we would like to invoke our program “merge.py”
 against the subset of 9 files the User selected whose result is an output
of one file.

How would the xml look?

Thanks!
George Weingart
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Re: [galaxy-dev] Problem uploading files to RNA-Rocket

[Dannon Baker]

Hey David,

I'm not sure why you'd be having this issue, but I'd contact the RNA-Rocket
server staff (pathporth...@vbi.vt.edu) for more assistance; this is not a
Galaxy server that the Galaxy Team manages.

-Dannon


On Thu, Aug 21, 2014 at 9:51 AM, David Salcines 
wrote:

> Hi, I was trying to upload some FASTQ files via FTP using the FileZilla
> client but although the program connects to the server it doesn't log in. I
> checked the user and the password several times and I tried to use another
> account but I still got the same error.
>
> I also tried to upload the files via URL (using Mega) but when the upload
> is finished the files appear to be empty.
>
> Thanks
> David
>
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[galaxy-dev] Problem uploading files to RNA-Rocket

[David Salcines]

Hi, I was trying to upload some FASTQ files via FTP using the FileZilla
client but although the program connects to the server it doesn't log in. I
checked the user and the password several times and I tried to use another
account but I still got the same error.

I also tried to upload the files via URL (using Mega) but when the upload
is finished the files appear to be empty.

Thanks
David
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