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://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
___________________________________________________________
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
greg@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/