Hi, I have made a lot of progress getting the LIMS system up and running and not I'm at the point where I was able to connect to the folders having my sequence data from galaxy. I can select a sample from a list of submitted samples in the tracking form and then match it to a file in our sequence directory. I get an error when trying to transfer the sample to galaxy. Does anybody have any ideas where should I start looking to fix this? Error below. Thanks in advance. Victor Last couple of lines are, NoSectionError: No section: 'data_transfer_user_login_info' On Oct 14, 2010, at 12:44 AM, Bossers, Alex wrote:
If I understand you correctly what you want to do you should be able to just do that by a tool.xml config calling an R script and providing a data file. The R script can open that file and process it into some output file known by galaxy.... But maybe I oversee something.
In your tool_config grab an R-file and some datafile:
<command> R --slave -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
Hope this helped,
Alex
________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Freddy [freddy.debree@wur.nl] Verzonden: woensdag 13 oktober 2010 14:19 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] rpy or perl
I am not using perl, but bash, which makes things much easier on the cmd line. However, maybe you know how to retrieve the R output or: what exactly is the problem for Galaxy for how to handle the system output from R through the shell? We have seen it here with other tools as well. R should work straight from the cmd line as well. And everything - incl R - does when use bash in a shell, but as soon as you put galaxy in between you and the program the output, is nowhere to be seen
so far, we've been able to simply 'mv' the output from the program towards bash and that will push it to galaxy. But with R this didn't work. (so far)
On 10/13/2010 12:47 PM, Leandro Hermida wrote:
Just to note for those Perl people developing tools with Galaxy and wanting to interface with R there are a couple of libraries out there to do this for you:
RSPerl http://www.omegahat.org/RSPerl/
Statistics::R http://search.cpan.org/search?query=Statistics%3A%3AR
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Error Traceback: View as: Interactive | Text | XML (full) ⇝ NoSectionError: No section: 'data_transfer_user_login_info' URL: http://mir-13:8087/requests_admin/manage_datasets?sort=-create_time&operation=Start+Transfer&id=df7a1f0c02a5b08e Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.framework:139 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.requests_admin:469 in manage_datasets view self.__start_datatx(trans, sample_dataset.sample, id_list) Module galaxy.web.controllers.requests_admin:837 in __start_datatx view datatx_user = self.__setup_datatx_user(trans, sample.library, sample.folder) Module galaxy.web.controllers.requests_admin:739 in __setup_datatx_user view email = config.get("data_transfer_user_login_info", "email") Module ConfigParser:511 in get view << except KeyError: if section != DEFAULTSECT: raise NoSectionError(section) # Update with the entry specific variables if vars: NoSectionError: No section: 'data_transfer_user_login_info'
