On 11/10/11 06:25, Greg Von Kuster wrote:
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()



Hi Greg,

Both changes you made look good. Thanks!

The reason I had broken the Grinder wrapper into 2 script executions is that the first script is very generic can be used by other tools (until issue 325 is resolved), while the second is very specific to Grinder since it renames its files so that Galaxy detects the dynamic output files.

But, really, the dynamic output files is not needed, and, as far as I understand, prevents Grinder from being used efficiently in a workflow (only the first, dummy output is shown). From the wiki page http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files, I'd like to use the method "Variable Static Outputs determined by parameter values" because it is recommended over the method I use and because I assume that it is compatible with workflows.

But maybe I need a little bit of guidance with this because the example shown, the user is given a _limited_ number of output datasets to choose from. The Grinder case seems simple: give the user a field where he can specify the number of output he wants, say, 2, 10, or 100 and produce as many datasets as needed. So, in the <output> section, the only reasonable way to process the output would be to have some sort of loop. Is this possible?

Thank you,

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://fangly@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


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