That would all be terrific. Thanks Greg!
Florent

On 07/10/11 10:15, Greg Von Kuster wrote:
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 <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 <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


___________________________________________________________
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu <mailto: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 <http://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 <mailto:g...@bx.psu.edu>




___________________________________________________________
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