Hello Florent,

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

> Hi Greg,
> 
> Thank you for your help. Your suggestion worked like a charm!
> 
> I was expecting to see an error because I did not create the ../shed_tool/ 
> folder that contains the tools installed from the shed, but I was happy to 
> see that it was automatically created.
> 
> 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.

Change set 6095:540ff06d44b4 allows for both "tool_config_file" and 
"tool_config_files" to behave the same way.


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

Fixed in change set 6095:540ff06d44b4.


> 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 this a bit more now that I'm back in the lab and feel 
differently than I did when I initially looked at it - I was on vacation, after 
all ;)

Galaxy automatically adds the path to the tool config file (in your case, 
ginder.xml), no matter where it is located, so your $tool_dir setting is really 
not necessary.  To simplify the discussion, I'll remove the if blocks from your 
command, and add an interpreter attribute.  So we have something like:

  <command interpreter="python">
    stderr_wrapper.py grinder grinder_multiple_outputs.py $output_dir $base_name
  </command>

The problem with the above is that the use of the interpreter attribute applies 
only to stderr_wrapper.py, but not grinder_multiple_outputs.py.  However, your 
stderr_wrapper.py and grinder_multiple_outputs.py do not have to be a separate 
scripts, but can merged into one overall script that uses the same approach as 
the ~/tools/gatk/gatk_wrapper.py script (among several other examples in the 
Galaxy distribution).  Doing this would allow for something like the following:

<command interpreter="python">
  grinder_wrapper.py -reference_file<etc> $output_dir $base_name
</command>

The code inside grinder_wrapper.py would parse the command line, and call the 
required grinder binary itself.  It could also include code like the following, 
eliminating the need for the separate stderr_wrapper.py.

    #set up stdout and stderr output options
    stdout = open_file_from_option( options.stdout, mode = 'wb' )
    stderr = open_file_from_option( options.stderr, mode = 'wb' )
    #if no stderr file is specified, we'll use our own
    if stderr is None:
        stderr = tempfile.NamedTemporaryFile( prefix="grinder-stderr-", 
dir=tmp_dir )
    
    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, 
shell=True, cwd=tmp_dir )
    return_code = proc.wait()
    
    if return_code:
        stderr_target = sys.stderr
    else:
        stderr_target = sys.stdout
    stderr.flush()
    stderr.seek(0)
    while True:
        chunk = stderr.read( CHUNK_SIZE )
        if chunk:
            stderr_target.write( chunk )
        else:
            break
    stderr.close()




> 
> 
>> <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
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>> 
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
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>>> please use the interface at:
>>> 
>>> http://lists.bx.psu.edu/
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
> 

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



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