Hello Florent,

Thanks for your comments and suggestions - see my inline comments.

On Oct 4, 2011, at 11:42 PM, Florent Angly wrote:

> Hi Greg,
> 
> I have a few additional comments and questions though:
> 1/ In the universe_wsgi.ini file, maybe the tool_config_file parameter could 
> be renamed to tool_config_files (plural) to indicate that it takes a list of 
> files.

I considered this, but held off on making this change since it would require 
all local Galaxy installations to change as well.  I'll soon enhance the 
setting to behave the same way for both terms (tool_config_file or 
tool_config_files) , so backward compatibility will not be a problem and using 
the plural term will be more clear.  Thanks for the suggestion.

> 2/ It seems like the Tools Search box cannot find newly installed tools. 
> However, after I restart Galaxy, it works as intended again.

I haven't got the search hooked up to the installed tools yet, but will very 
soon.  Thanks for finding and reporting this issue.


> 3/ In the Grinder wrapper, I relied on installing the wrapper under a 
> specific folder: ./tools/ngs simulation/grinder. The new wrapper installation 
> procedure installs the tools in the ../shed_tools/ folder and the admins can 
> choose under what category the tool is to be placed. This means that my 
> Grinder wrapper fails since it does not know where to find the scripts it 
> needs. Is there a way to get the directory where a tool is installed? Here is 
> an excerpt of the Grinder wrapper so you can better understand what I am 
> trying to do. This wrapper first runs Grinder and then moves its files (the 
> number of files is hard to determine ahead of time) to a place where Galaxy 
> will find them (see the wiki page 
> http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files under section 
> "Number of Output datasets cannot be determined until tool run").

I've looked at your tool, and I think it would be beneficial if I provided 
something like ${tool.install_dir}.  This feature would allow you to eliminate 
the use of hard-coded paths in your tools like the following which can 
generally be counted on to break at some point.  I should have this feature 
available fairly soon ( I'm out of the lab this week, but will be back next 
week ).  Your tool should then be enhanced to use this new feature - I'll let 
you know when it's available.

#set $tool_dir = os.path.join( os.path.abspath($__root_dir__), 'tools', 
'ngs_simulation' )


> 
> Thanks,
> 
> Florent
> 
> 
>> <command>
>>    #set $tool_dir = os.path.join( os.path.abspath($__root_dir__), 'tools', 
>> 'ngs_simulation' )
>>    #set $script1  = os.path.join( $tool_dir, 'stderr_wrapper.py' )
>>    #set $script2  = os.path.join( $tool_dir, 'grinder_multiple_outputs.py' )
>> 
>>    $script1
>>      grinder
>>      #if $reference_file.specify == "builtin":
>>        -reference_file   ${ filter( lambda x: str( x[0] ) == str( 
>> $reference_file.value ), $__app__.tool_data_tables[ 'all_fasta' 
>> ].get_fields() )[0][-1] }
>>      #else if $reference_file.specify == "uploaded":
>>        -reference_file   $reference_file.value
>>      #end if
>>      [...]
>>      #if str($homopolymer_dist):
>>        -homopolymer_dist $homopolymer_dist
>>      #end if
>> 
>>      #set $output_dir = $__new_file_path__
>>      -output_dir         $output_dir
>> 
>>      #set $base_name  = $output.id
>>      -base_name          $base_name
>>    ;
>> 
>>    $script2 $output_dir $base_name
>> 
>> </command>
> 
> 
> 
> On 04/10/11 22:55, Greg Von Kuster wrote:
>> Hello Florent,
>> 
>> Sorry for the confusion on this - we are preparing a new Galaxy 
>> distribution, and the tool shed wiki has been written in preparation for it. 
>>  The new distribution will be available fairly soon, and the Galaxy News 
>> Brief will include information about these new tool shed features.  In any 
>> case, you have already discovered that you can use in if you update your 
>> Galaxy instance to the latest Galaxy development repository ( Galaxy central 
>> ).
>> 
>> The problem you see is most likely caused by your not having configured an 
>> additional tool_config_file setting in your universe_wsgi.ini.  Look for 
>> something like following in your latest version of the 
>> universe_wsgi.ini.sample that you got when you updated from Galaxy central.
>> 
>> # Locally installed tools and tools installed from tool sheds
>> tool_config_file = tool_conf.xml,shed_tool_conf.xml
>> 
>> If you add a new additional file name like shed_tool_conf.xml, you should 
>> not have a problem installing from a tool shed.  I'll have a fix for the bug 
>> you've discovered shortly, but making this change will fix the behavior 
>> until then.
>> 
>> Let me know if you bump into any additional problems.
>> 
>> Thanks for finding this!
>> 
>> Greg Von Kuster
>> 
>> On Oct 4, 2011, at 2:53 AM, Florent Angly wrote:
>> 
>>> Hi all,
>>> 
>>> I tried the latest stable version of Galaxy: 
>>> http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to 
>>> how to use the new tool shed including how to automatically deploy tools 
>>> from the shed in a local Galaxy server.
>>> The documentation mentioned some tool shed options available from the the 
>>> admin section of Galaxy but I could not locate these options in my instance 
>>> of galaxy. So my question is: Can one only take advantage of the tool 
>>> deployment from the shed in the development version of Galaxy? If so, I 
>>> think the Tool shed wiki should be more clear about this.
>>> 
>>> Then I tried the latest development version of Galaxy and could locate the 
>>> tool shed deployment options. I attempted to install the Grinder wrapper 
>>> (http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp=community&id=3d8312720a69a558&f-deleted=False&show_item_checkboxes=false&async=false&operation=view_or_manage_repository&f-free-text-search=grinder&page=1<http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=name&webapp=community&id=3d8312720a69a558&f-deleted=False&show_item_checkboxes=false&async=false&operation=view_or_manage_repository&f-free-text-search=grinder&page=1>)
>>>  but ran into an error that I am pasting below:
>>>> URL: 
>>>> http://localhost:8080/admin/install_tool_shed_repository?tool_shed_url=toolshed.g2.bx.psu.edu&name=grinder&description=Genomic,%20metagenomic%20and%20amplicon%20read%20simulator&repository_clone_url=http://fan...@toolshed.g2.bx.psu.edu/repos/fangly/grinder&changeset_revision=5ba7c9ac056a
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
>>>>  line 364 in respond
>>>>  app_iter = self.application(environ, detect_start_response)
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
>>>>  line 98 in __call__
>>>>  environ, self.app)
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
>>>>  line 539 in intercept_output
>>>>  app_iter = application(environ, replacement_start_response)
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>>>>  line 80 in __call__
>>>>  return self.application(environ, start_response)
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>>>>  line 632 in __call__
>>>>  return self.application(environ, start_response)
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/base.py',
>>>>  line 160 in __call__
>>>>  body = method( trans, **kwargs )
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/framework/__init__.py',
>>>>  line 173 in decorator
>>>>  return func( self, trans, *args, **kwargs )
>>>> File 
>>>> '/home/floflooo_mint/Software/galaxy-central/lib/galaxy/web/controllers/admin.py',
>>>>  line 805 in install_tool_shed_repository
>>>>  shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' 
>>>> )
>>>> IndexError: list index out of range
>>> I get the same problem with other wrappers such as FastQC. Am I doing 
>>> something wrong?
>>> 
>>> Thanks,
>>> 
>>> Florent
>>> 
>>> 
>>> ___________________________________________________________
>>> The Galaxy User list should be used for the discussion of
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>>> at usegalaxy.org.  Please keep all replies on the list by
>>> using "reply all" in your mail client.  For discussion of
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>>> use the Galaxy Development list:
>>> 
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
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>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
> 
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
> http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
> http://lists.bx.psu.edu/

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu



___________________________________________________________
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