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(a)lists.bx.psu.edu [galaxy-dev-bounces(a)lists.bx.psu.edu] namens
Freddy [freddy.debree(a)wur.nl]
Verzonden: woensdag 13 oktober 2010 14:19
Aan: galaxy-dev(a)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&o...
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'