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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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Variabels in label elements
by Bossers, Alex 09 Nov '10

09 Nov '10

Hi All, Does someone know how to get the value of a type="select" param_name displayed in the output file label? I know how to do it if its just a non-nested param setup-up using ${input1.value_label} where the input1 is the select_name. But this fails if the select is inside a conditional..... From cheetah script I can call these values like IF $tool.cmd=="something":..... But whatever I try in the <outputs><data> fails (I though it to be ${tool.cmd.value_label} but that complains on cmd not defined.... All possible iteration tried :( Snippet of a generalised tool.xml below. Any suggestions or hints where to get documentation on this syntax is welcomed! Alex <command> /opt/tools/$tool.cmd $cmd_extra $input_delta #if $tool.cmd=="show-aligns": $tool.extra1 $tool.extra2 #end if > $out_tool </command> <inputs> <conditional name="tool"> <param name="cmd" type="select" value="show-snps" label="Select tool" > <option value="show-snps">show snps</option> <option value="show-aligns">show aligns</option> </param> <when value="show-aligns"> <param name="extra1" type="text" size="40" value="" label="IdR" help="FastA header ref sequence" /> <param name="extra2" type="text" size="40" value="" label="IdQ" help="FastA header query sequence" /> </when> <when value="show-snps" /> </conditional> <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" /> <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="see specific cmd line options below for each tool" /> </inputs> <outputs> <data name="out_tool" format="text" label="tool ${tool.cmd.value_label}" /> </outputs>

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How to implement the button "send query to galaxy" in UCSC Main tool
by Zhe Chen 09 Nov '10

09 Nov '10

Hi, How to implement the button "send query to galaxy" in (Get Data)->(UCSC Main tool) on the second page? Do you have a code example of it? Thanks

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Re: [galaxy-dev] [galaxy-bugs] report the error
by Jeremy Goecks 08 Nov '10

08 Nov '10

Hi Mingquan, Please send your queries to one of our mailing lists -- galaxy-dev or galaxy-user -- rather than to individuals. That way, more people can see and help you with your questions, you'll likely get a more timely response, and the mailing list archive can serve as a useful repository. Your question about GFF to BED is best addressed to galaxy-user (b/c it's about usage of Galaxy), and your question about Tophat is best addressed to galaxy-dev (b/c it's about setting up a local Galaxy instance). Hence, I've cc'd both lists. Ok, on to your questions: > Maybe i can use the tophat anlone. We've got a Galaxy wrapper ready for Tophat version 1.1+ ; it will likely be available in galaxy-central this week. Once you update your version of Galaxy, you'll be able to run Tophat in Galaxy. > But now i have a another question for giff to bed function. > i want to use gff-to-bed function after i run it, it seems that i got the results : > > empty, format: bed, database: ? > Info: 0 lines converted to BED. Skipped 74166 blank/comment/invalid lines starting with line #1. > > i am using gff3 file.and it is the first few lines. > > ##gff-version 3 > ##genome-build MSU Rice Genome Annotation Project osa1r6 > ##species Oryza sativa spp japonica cv Nipponbare > ##sequence-region Chr1 1 43268879 > > Chr1 MSU_osa1r6 gene 1903 9817 . + . ID=13101.t00001;Name=TBC%20domain%20containing%20protein%2C%20expressed;Alias=LOC_Os01g01010 > Chr1 MSU_osa1r6 mRNA 1903 9817 . + . ID=13101.m00001;Parent=13101.t00001;Alias=LOC_Os01g01010.1 > > Chr1 MSU_osa1r6 five_prime_UTR 1903 2268 . + . Parent=13101.m00001 > Chr1 MSU_osa1r6 five_prime_UTR 2354 2448 . + . Parent=13101.m00001 This appears to be a valid GFF3 file and should work fine. We'll look into this and get back to you. Thanks, J.

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