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