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() > > >> <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 >>> >>> >>> ___________________________________________________________ >>> 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 >> g...@bx.psu.edu >> >> >> > Greg Von Kuster Galaxy Development Team g...@bx.psu.edu
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