Re: [galaxy-dev] Parameter Storing in Database

[Katherine Beaulieu]

On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> No actually I meant in what file is the table job_parameter getting filled
> during execution?
> Katherine
>
> On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden  wrote:
>
>> You mean the stuff for the tool-data tables? As I understand it, it is
>> loaded in:
>>
>> lib/galaxy/tools/data/__init__.py
>>
>> There's a ToolDataTableManager and a TabularToolDataTable (with
>> associated TabularToolDataField).
>>
>> Peter
>>
>> On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu <
>> katherine.beaulieu...@gmail.com> wrote:
>>
>>> Would anyone be able to tell me in what file the storing of tool
>>> parameters into the database occurs?
>>> Thanks!
>>> Katherine
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Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

[Steve Cassidy]

Nah, definitely baby steps…

so, in the repo you point to there seems to be an error in the Dockerfile, the 
ENV line should use the var=value syntax to have more than one setting on one 
line (maybe that’s changed recently in docker).

with this I built a new docker image, when I run my first tool it takes an age 
while it’s installing the deps, then it crashes with:

Traceback (most recent call last):
  File 
"/export/galaxy-central/database/job_working_directory/000/1/set_metadata_QUJQLD.py",
 line 1, in 
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
  File "/galaxy-central/lib/galaxy_ext/metadata/set_metadata.py", line 23, in 

from sqlalchemy.orm import clear_mappers
ImportError: No module named sqlalchemy.orm

and the output:

discarding /galaxy-central/tool_deps/_conda/bin from PATH
prepending 
/export/galaxy-central/database/job_working_directory/000/1/conda-env/bin to 
PATH
discarding /galaxy-central/tool_deps/_conda/bin from PATH
prepending 
/export/galaxy-central/database/job_working_directory/000/1/conda-env/bin to 
PATH

I’m guessing this is some kind of conflict between python versions in and out 
of conda environments? Surely sqlalchemy would be installed for Galaxy to work? 
 

I’ll try to dig around this in the morning but if it rings a bell…

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

> On 25 Aug 2016, at 8:43 PM, Björn Grüning  wrote:
> 
> Hi Steve,
> 
> you call this baby-steps? I think this is huge! :)
> 
> All what you are missing is to enable conda in Galaxy.
> Look at Gregs new flavour which is entirely Conda/Galaxy based.
> 
> You need to enable these env vars to make Galaxy conda enabled:
> 
> https://github.com/gregvonkuster/docker-galaxy-csg/blob/master/Dockerfile#L9
> 
> Hope this helps,
> Bjoern
> 
> Am 25.08.2016 um 12:32 schrieb Steve Cassidy:
>> Hi all,
>>  I’m making baby steps towards having a repeatable installation for my
>> tools.  But I’m now stuck, so help would be appreciated.
>> 
>> I have a tool that works and is in the test toolshed (alveoimport in
>> Data Sources). 
>> 
>> It depends on my python package which is now part of bioconda (pyalveo,
>> version 0.6). 
>> 
>> I can run my tool via planemo, which works I think because I have
>> pyalveo installed in a local venv.  
>> 
>> If I try to run the docker image (derived from  bgruening/galaxy-stable
>> but with the testtoolshed added) I am able to install my tool, but it
>> doesn’t pick up the dependency, so it doesn’t work. 
>> 
>> I tried running with planemo turning on conda dependency resolution
>> (following https://pypi.python.org/pypi/planemo/): 
>> 
>> planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution .
>> 
>> It seems to have a go, but fails:
>> 
>> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency
>> shell command for dependency 'pyalveo'
>> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo
>> version 0.6
>> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
>> 
>> (isnull? True)
>> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
>> 
>> (isnull? True)
>> galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve
>> dependency on 'pyalveo', ignoring
>> 
>> So, what’s the easiest route to a Galaxy deployment with my tool
>> installed. The Docker route would be best I think, but what do I have to
>> add to bgruening/galaxy-stable to have conda find my dependencies.
>> 
>> Thanks in advance,
>> 
>> Steve
>> 
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>> 
>> 
>> 
>> 
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>> 

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Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

[Björn Grüning]

Hi Steve,

you call this baby-steps? I think this is huge! :)

All what you are missing is to enable conda in Galaxy.
Look at Gregs new flavour which is entirely Conda/Galaxy based.

You need to enable these env vars to make Galaxy conda enabled:

https://github.com/gregvonkuster/docker-galaxy-csg/blob/master/Dockerfile#L9

Hope this helps,
Bjoern

Am 25.08.2016 um 12:32 schrieb Steve Cassidy:
> Hi all,
>   I’m making baby steps towards having a repeatable installation for my
> tools.  But I’m now stuck, so help would be appreciated.
> 
> I have a tool that works and is in the test toolshed (alveoimport in
> Data Sources). 
> 
> It depends on my python package which is now part of bioconda (pyalveo,
> version 0.6). 
> 
> I can run my tool via planemo, which works I think because I have
> pyalveo installed in a local venv.  
> 
> If I try to run the docker image (derived from  bgruening/galaxy-stable
> but with the testtoolshed added) I am able to install my tool, but it
> doesn’t pick up the dependency, so it doesn’t work. 
> 
> I tried running with planemo turning on conda dependency resolution
> (following https://pypi.python.org/pypi/planemo/): 
> 
> planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution .
> 
> It seems to have a go, but fails:
> 
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency
> shell command for dependency 'pyalveo'
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo
> version 0.6
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
> 
> (isnull? True)
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
> 
> (isnull? True)
> galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve
> dependency on 'pyalveo', ignoring
> 
> So, what’s the easiest route to a Galaxy deployment with my tool
> installed. The Docker route would be best I think, but what do I have to
> add to bgruening/galaxy-stable to have conda find my dependencies.
> 
> Thanks in advance,
> 
> Steve
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
> 
> 
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[galaxy-dev] Putting it all together - toolshed tool + conda dependency

[Steve Cassidy]

Hi all,
  I’m making baby steps towards having a repeatable installation for my tools.  
But I’m now stuck, so help would be appreciated.

I have a tool that works and is in the test toolshed (alveoimport in Data 
Sources).

It depends on my python package which is now part of bioconda (pyalveo, version 
0.6).

I can run my tool via planemo, which works I think because I have pyalveo 
installed in a local venv.

If I try to run the docker image (derived from  bgruening/galaxy-stable but 
with the testtoolshed added) I am able to install my tool, but it doesn’t pick 
up the dependency, so it doesn’t work.

I tried running with planemo turning on conda dependency resolution (following 
https://pypi.python.org/pypi/planemo/):

planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution .

It seems to have a go, but fails:

galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency shell 
command for dependency 'pyalveo'
galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo version 
0.6
galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned 
 (isnull? 
True)
galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned 
 (isnull? 
True)
galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve dependency 
on 'pyalveo', ignoring

So, what’s the easiest route to a Galaxy deployment with my tool installed. The 
Docker route would be best I think, but what do I have to add to 
bgruening/galaxy-stable to have conda find my dependencies.

Thanks in advance,

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

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Re: [galaxy-dev] problem with local toolshed

[Vincent Cahais]

It works, thank you.

Vincent

Le 24/08/2016 à 17:24, Martin Čech a écrit :
Hello Vincent,

This looks like an encoding problem we we can fix. Could you please try the 
following patch?

https://gist.github.com/martenson/22f6efc7cd577ea6af85a11694091d5f

Thanks,

Martin

On Wed, Aug 24, 2016 at 5:17 AM Vincent Cahais 
> wrote:

Hello,

I cannot use my toolshed anymore because of a bug.

The service is running, but the web page display this error :

Module galaxy.web.framework.middleware.error:151 in __call__
>>   app_iter = self.application(environ, 
>> sr_checker)
Module paste.recursive:85 in __call__
>>   return self.application(environ, 
>> start_response)
Module galaxy.webapps.tool_shed.framework.middleware.hg:218 in __call__
>>   return self.app( environ, start_response )
Module paste.httpexceptions:640 in __call__
>>   return self.application(environ, 
>> start_response)
Module galaxy.web.framework.base:131 in __call__
>>   return self.handle_request( environ, 
>> start_response )
Module galaxy.web.framework.base:190 in handle_request
>>   body = method( trans, **kwargs )
Module galaxy.webapps.tool_shed.controllers.repository:1963 in index
>>   status=status )
Module galaxy.web.framework.webapp:858 in fill_template
>>   return self.fill_template_mako( filename, 
>> **kwargs )
Module galaxy.web.framework.webapp:872 in fill_template_mako
>>   return template.render( **data )
Module mako.template:445 in render
>>   return runtime._render(self, self.callable_, 
>> args, data)
Module mako.runtime:829 in _render
>>   **_kwargs_for_callable(callable_, data))
Module mako.runtime:864 in _render_context
>>   _exec_template(inherit, lclcontext, 
>> args=args, kwargs=kwargs)
Module mako.runtime:890 in _exec_template
>>   callable_(context, *args, **kwargs)
Module _base_base_panels_mako:123 in render_body
>>   __M_writer(unicode(self.left_panel()))
Module _webapps_tool_shed_index_mako:166 in render_left_panel
>>   
>> __M_writer(filters.html_escape(unicode(trans.app.shed_counter.generation_time
>>  )))
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 2: ordinal 
not in range(128)

Thanks,

Vincent

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