Re: [galaxy-user] Problem with new tool shed
Hello Forent, On Oct 13, 2011, at 2:48 AM, Florent Angly wrote: 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? This is not yet possible. This is something that has been desired for some time, but is not on our near-future plans for implementation. Thank you, Florent Greg Von Kuster Galaxy Development Team 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. 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/
Re: [galaxy-user] Problem with new tool shed
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
Re: [galaxy-user] Problem with new tool shed
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=namewebapp=communityid=3d8312720a69a558f-deleted=Falseshow_item_checkboxes=falseasync=falseoperation=view_or_manage_repositoryf-free-text-search=grinderpage=1http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=namewebapp=communityid=3d8312720a69a558f-deleted=Falseshow_item_checkboxes=falseasync=falseoperation=view_or_manage_repositoryf-free-text-search=grinderpage=1)
but ran into an error that I am pasting below:
URL:
