November 2010 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] [galaxy-user] plugging R into galaxy
by Peter 12 Nov '10

12 Nov '10

On Fri, Nov 12, 2010 at 1:09 PM, Anthony Ferrari <ferraria(a)gmail.com> wrote: > OK. I have made some tests this morning to figure this all out. > Indeed, the problem with ">" is that it catches every single message R sends > to STDOUT and not only object of your interest, so this is definitely not a > reliable solution. Solution suggests by Alex worked perfectly well. > I would suggest also to use the 'trailingOnly=TRUE' option within the > commandArgs() call in the R script. That allows you to only care about the > args given after the '--args' option. You can then forget how many previous > options you have in your command line (--vanilla, --slave, -f or others...). > First parameter useful to your R script would then be > commandArgs(trailingOnly=T)[1] and so on. That is a very handy tip, commandArgs(trailingOnly=T), thanks! > There is just another little point that I would like to clarify. At the > beginning my tests didn't work at all and I realize that I have to give the > full path to the R script (in the command tag) to make it work. What happens if you do <command> rather than <command interpreter="bash">? Peter P.S. Cross posted to Galaxy-dev, could we continue this there?

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Dataset search suggestion
by SHAUN WEBB 12 Nov '10

12 Nov '10

I now have a large number of datasets saved under my account and it is difficult to find previous datasets that I need for new histories. It would be useful to be able to search by history name,tags,annotation in the advanced set. I tend to add tags and meaningful names to each history but it is rather tedious to annotate and tag every dataset. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Getting problem while executing program by using DRMAA_PYTHON package
by hari krishna 12 Nov '10

12 Nov '10

This is my program example.py .... when i trying to execute this code am getting error as shown below.... can u please help anything for proceeding further.... my python version is 2.4 and ctype that i installed is pygame-ctypes-0.09... #!/usr/bin/env python import drmaa def main(): """Create a drmaa session and exit""" s=drmaa.Session() s.initialize() print 'A session was started successfully' s.exit() if __name__=='__main__': main() ~ [gridmon@g8 DRMAA]$ python example.pyc Traceback (most recent call last): File "example.py", line 3, in ? import drmaa ImportError: No module named drmaa [gridmon@g8 DRMAA]$ cd drmaa-0.4b3 [gridmon@g8 drmaa-0.4b3]$ python example.pyc Traceback (most recent call last): File "example.py", line 3, in ? import drmaa File "/home/gridmon/DRMAA/drmaa-0.4b3/drmaa/__init__.py", line 30, in ? import ctypes as _ct ImportError: No module named ctypes -- Thanks & Regards, Hari Krishna .M

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Classic alignment tools (ClustalW, MUSCLE, T-Coffee, etc)
by Peter 11 Nov '10

11 Nov '10

Hello all, I've looked at the provided Galaxy wrappers, and the Galaxy Tool Shed, http://community.g2.bx.psu.edu/ but haven't seen any "classic" multiple alignment tools wrapped for Galaxy. To be clear I'm talking about things like ClustalW, MUSCLE, T-Coffee, and so on (not tools for mapping sequencing reads onto a reference genome). Is anyone working on this sort of thing in Galaxy? Thanks, Peter

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GTF sniffer
by SHAUN WEBB 11 Nov '10

11 Nov '10

I have a tool that uses .gtf input, when I upload a .gtf file it is automatically recognised as a .gff file meaning I have to manually change the format to gtf. I know gff and gtf are very similar but is it possible to have a gtf sniffer? Out of interest is there any documentation relating to writing sniffers for different datatypes I should probably have a go at writing a few for my on. Thanks. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Problem with <command> tag
by Zhe Chen 10 Nov '10

10 Nov '10

Hi, When I put the following in my tool xml <command>perl rpc_client.pl -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat "sequencesText" "$sequence"</command> And run the tool, it only execute " perl rpc_client.pl "sequencesText" "$sequence" ". Those options " -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat " are ignored. How to fix this problem? Thanks

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Re: [galaxy-dev] [galaxy-user] plugging R into galaxy
by Bossers, Alex 10 Nov '10

10 Nov '10

Hi Anthony, good you have it going. The example showed how to load a user provided R script (which might be a security issue but ok for testing). We normally would specify the R script with path to the tools dir. This has the advantage you can change and test your script without having to refresh your running tools in galaxy. The example is correct. The Provided R script in this case gets both the arguments $in_data AND $out_data into R by the args[6 and 7]. So output of the R script is directly pulled and put into the correct expected file without any mv statements in bash shell or whatever. The > would be used if output is at STDOUT. Freddy made a good comment on the WARNINGS! You have to capture them and either trash them to /dev/null (or &-) or append them to a log file (usually STDERR can be captured by 2>&- or 2>>./somelogfile.log). If you don't take care of it they will give you a red history box even when all was fine and just a warning so you have to deal with that... accounts for more tools than just R by the way. Cheers, Alex ________________________________ Van: Anthony Ferrari [ferraria(a)gmail.com] Verzonden: woensdag 10 november 2010 19:12 Aan: Bossers, Alex CC: galaxy-user(a)lists.bx.psu.edu Onderwerp: Re: [galaxy-user] plugging R into galaxy Thanks to all for your comments. Alex, I have done something similar to what your suggest except that I use Rscript executable embedded in a script shell. There is something I don't understand when reading your example. How galaxy understands that is has to store your write.table() call in your $out_data variable ? Didn't you forget to redirect your R output stream with ">" ? <command> R –slave --vanilla -f $in_r --args $in_data > $out_data </command> Anthony On 9 November 2010 20:32, Bossers, Alex <Alex.Bossers(a)wur.nl<mailto:Alex.Bossers@wur.nl>> wrote: Anthony, We had some discussion on the galaxy dev list about R. See for instance my posting of Oct 14th and several others as well (for ref sake a snippet is attached below). That example opens an R script outside tool config (in this case a script that opens an input file and generates some output file which is grabbed by galaxy). Hope this helps, Alex <command> R –slave --vanilla -f $in_r --args $in_data $out_data </command> <inputs> <param name="in_data" type="data" format="tabular" label="Test data file" /> <param name="in_r" type="data" format="text" label="R script to load and execute" /> </inputs> <outputs> <data name="out_data" type="data" format="tabular" label="R script output" /> </outputs> The R script provided will grab the args from the cmd line as you indiciated earlier: # R script file to grab input and output filenames from cmdline and just copy args <- commandArgs() output <- read.table(args[6], header=T) write.table(output,sep="\t",file=args[7],row.names=F) #end script Van: galaxy-user-bounces(a)lists.bx.psu.edu<mailto:galaxy-user-bounces@lists.bx.psu.edu> [mailto:galaxy-user-bounces@lists.bx.psu.edu<mailto:galaxy-user-bounces@lists.bx.psu.edu>] Namens Anthony Ferrari Verzonden: dinsdag 9 november 2010 15:21 Aan: galaxy-user(a)lists.bx.psu.edu<mailto:galaxy-user@lists.bx.psu.edu> Onderwerp: [galaxy-user] plugging R into galaxy Dear galaxy users, My team is involved in the NGS field. We have our own local cluster and we are looking for a workflow management system. Currently we are trying to set up and test galaxy. For our quality control analysis pipeline, R statistical software will be used. So we want to be able to call R scripts from galaxy. I know that it is possible and the xy_plot.xml is a really good example (conditional & when, repeat tags). Also, in this example a <configfile> tag is used. Within this tag you put your R code. And moreover you can add lines beginning with only one '#' which will be interpreted with cheetah template engine. This is helpful to create dynamic content of your R code with respect to your submitted parameters. (an old screencast introduces this example) My question is : is there a way to avoid the <configfile> section and to let all the R code be outside the tool's xml config file? If yes, how can we specify an output file in the xml conf that will catch, for instance, a write.table() call in the R script ? Best regards, Anthony

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relative links to static pages broken for proxied web server
by David Hoover 10 Nov '10

10 Nov '10

I'm serving the static pages for Galaxy in a subdirectory, and links like ../static/images/maf_icons/interval2maf.png are broken, because ../ is not matched in the regular expression block of the Apache configuration. The links should be absolute paths, not relative paths. David Hoover Helix Systems Staff http://helix.nih.gov

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Error downloading workflow
by Jesse Erdmann 10 Nov '10

10 Nov '10

All, I am having trouble downloading relatively complex workflows. The problem happens when I have a task in the workflow with multiple outputs being renamed. Here is the XML of the stack trace I get: <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.6.6"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /Users/jerdmann/Python/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /Users/jerdmann/Python/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /Users/jerdmann/Python/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /Users/jerdmann/Python/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /Users/jerdmann/Python/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /Users/jerdmann/Python/galaxy-central/lib/galaxy/web/framework/base.py </filename> <line> 145 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /Users/jerdmann/Python/galaxy-central/lib/galaxy/web/framework/__init__.py </filename> <line> 74 </line> <function> decorator </function> <operation> return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) </operation> <operation_context> def decorator( self, trans, *args, **kwargs ): trans.response.set_content_type( "text/javascript" ) return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) if not hasattr(func, '_orig'): decorator._orig = func </operation_context> </frame> <frame> <module> galaxy.web.framework </module> <filename> /Users/jerdmann/Python/galaxy-central/lib/galaxy/web/framework/__init__.py </filename> <line> 84 </line> <function> decorator </function> <operation> return func( self, trans, *args, **kwargs ) </operation> <operation_context> def decorator( self, trans, *args, **kwargs ): if trans.get_user(): return func( self, trans, *args, **kwargs ) else: return trans.show_error_message( </operation_context> </frame> <frame> <module> galaxy.web.controllers.workflow </module> <filename> /Users/jerdmann/Python/galaxy-central/lib/galaxy/web/controllers/workflow.py </filename> <line> 1049 </line> <function> export_to_file </function> <operation> stored_dict = self._workflow_to_dict( trans, stored ) </operation> <operation_context> # Stream workflow to file. stored_dict = self._workflow_to_dict( trans, stored ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' sname = stored.name </operation_context> </frame> <frame> <module> galaxy.web.controllers.workflow </module> <filename> /Users/jerdmann/Python/galaxy-central/lib/galaxy/web/controllers/workflow.py </filename> <line> 1516 </line> <function> _workflow_to_dict </function> <operation> step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) </operation> <operation_context> input_type = type( val ) if input_type == RuntimeValue: step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) elif input_type == dict: # Input type is described by a dict, e.g. indexed parameters. </operation_context> </frame> </stack> <exception> <type> TypeError </type> <value> 'WorkflowStep' object is unsubscriptable </value> </exception> </traceback> -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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Aspera
by lentaing＠jimmy.harvard.edu 09 Nov '10

09 Nov '10

Hi, Are there any plans to integrate galaxy with aspera? In other words, are there any plans to allow users to configure their own galaxy instance to use an aspera server for downloading and uploading files? Thanks, Len

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