Hi ,
I am trying to create a metadata for or taking input for our tool.
Matadata should take (1primary + 4 composite files)
I have read the documentation and created a metadata called “conf”.
class Configuration ( Data ):
file_ext = "conf"
composite_type = "basic"
MetadataElement( name="data_lines", default=4, desc="Number of data lines", readonly=True, optional=True, visible=True, no_value=0 )
def __init(self, **kwd):
Data.__init(self,**kwd)
self.add_composite_file('mapfile.txt')
self.add_composite_file('frequenctfile.txt')
self.add_composite_file('datafile.txt')
self.add_composite_file('pedfile.txt')
def init_meta(self,dataset,copy_from=None ):
Data.init_meta(self,dataset,copy_from=copy_from)
def generate_primary_file( self, dataset = None ):
rval = ['<html><head><title>Files for Composite Dataset (%s)</title></head><p/>This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext ) ]
for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) )
rval.append( '</ul></html>' )
return "\n".join( rval )
But after doing all this when I go to the text file formats in upload file and I click on the “conf” file format , the select box created to upload file is only 1.
Though I need 5 such select boxes. 1 for primary file and 4 other for the sub files.
Thanks a lot.
Regards,
Amit Modi
On 4/21/10 1:35 PM, "Modi, Amit" <Amit.Modi@nationwidechildrens.org> wrote:
Hi ,
Thanks a lot for the prompt reply.
Our tool in the normal course of execution produce messages on both stdout and stderr.But exits with a success status when successfully executed
So, does that means galaxy will always interpret this as job failure .
Is there any work around for this ?
Regards,
Amit Modi
On 4/21/10 1:13 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Modi, Amit wrote:
> Hi,
>
> I am almost done with integrating our tool with galaxy.
>
> It would be really great if you can help solve this issue as I was
> unable find anything related to this on the wiki.
>
> Our tool produces some output messages during its execution due to some
> reason galaxy splits them into 2 categories and displays as additional
> output and error messages though both of them are standard output
> messages ad should be displayed as additional output .
>
>
> Here is the snapshot of the message that is displayed.
>
> *Dataset 52: PPL File
> *
> Tool execution generated the following error message:
> 10/04/21 12:14:26 @0s, Initializing
> 10/04/21 12:14:26 @0s, Performing analysis
> 10/04/21 12:14:30 @4s, Analysis complete
> 10/04/21 12:14:30 @4s, Finished run
Hi Amit,
Are you sure that these messages are being printed to stdout? Galaxy
seems to be reading them from stderr.
--nate
>
> The tool produced the following additional output:
> 10/04/21 12:14:26 Use segment ID 4620291 for diagnostic purposes
> 10/04/21 12:14:26 kelvin V0.38.0 edit 2805 built Mar 25 2010 12:13:28
> 10/04/21 12:14:26 Compiler 4.1.1 20070105 (Red Hat 4.1.1-52)
> 10/04/21 12:14:26 Using GNU Scientific Library (GSL) statistical
> functions instead of internal ones
> 10/04/21 12:14:26 OpenMP-enabled w/maximum of 4 thread(s).
> 10/04/21 12:14:26 GCC optimization level 2 enabled
> 10/04/21 12:14:26 To check status (at some risk), type CTRL-\ or type
> "kill -3 28022"
> 10/04/21 12:14:26 Using configuration file
> /export/home/galaxy/galaxy-dist/database/files/000/dataset_151.dat
> 10/04/21 12:14:26 Computation is done in polynomial mode
> 10/04/21 12:14:26 polynomialScale is 1 (1-10, 1 is default)
> 10/04/21 12:14:26 Integration is done numerically (dkelvin)
> 10/04/21 12:14:26 Further progress will be displayed at 120 second intervals
> 10/04/21 12:14:26 9 pair(s) over a dynamic space (1LC) for 11 pedigree(s)
> 10/04/21 12:14:26 Trait-to-marker Two-Point, Dichotomous Trait, Equilibrium.
> 10/04/21 12:14:30 stopwatch overall(1) e:4s u:8s s:1s, vx:205780,
> ivx:15961, sf:14225, hf:0
>
>
> Also, the tool executes just fine and also produces the correct output
> files.
>
> I can verify these files by looking into the
> galaxy/galaxy-dist/database/files/000/ directory.
>
>
> But for some reason these files are not displayed on the web interface
> of galaxy and this error message is displayed along with failed status.
>
> Thanks a lot.
>
> Regards,
> Amit Modi
>
>
> On 4/19/10 11:34 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
>
> Modi, Amit wrote:
> > Hi,
> >
> >
> > We are trying to configure Galaxy to work with our tool.
> >
> > So far I have been able to configure it well and link it with the
> > cluster to do process all the jobs as per the documentation .
> >
> > Now what we want is the before the actual processing starts the
> > validations for the input files are done on the
> > Local. And the job processing is done on the cluster.
> >
> > Is there anyway we can configure this.
> >
> > We are using sge on the cluster.
>
> Hi Amit,
>
> I'm not sure what you mean by input file validation? You can have
> metadata set on the cluster by setting 'set_metadata_externally = True'
> in the config file. Additionally, the data source tools like Upload and
> UCSC can run on the cluster, providing the following are true:
>
> 1. The default directory used by Python's tempfile module is
> cluster-accessible (usually /tmp, so you can change it by setting $TEMP
> in the environment).
>
> 2. The cluster nodes have access to the Internet (NAT is fine).
>
> If this is not what you're looking for, please let us know.
>
> --nate
>
> >
> > Thanks a lot.
> >
> >
> >
> > Regards,
> > Amit Modi
> >
> >
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