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):
def init_meta(self,dataset,copy_from=None ):
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 =
opt_text = ''
opt_text = ' (optional)'
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.
On 4/21/10 1:35 PM, "Modi, Amit" <Amit.Modi(a)nationwidechildrens.org>
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 ?
On 4/21/10 1:13 PM, "Nate Coraor" <nate(a)bx.psu.edu> wrote:
Modi, Amit wrote:
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
Are you sure that these messages are being printed to stdout? Galaxy
seems to be reading them from stderr.
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
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
I can verify these files by looking into the
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.
On 4/19/10 11:34 AM, "Nate Coraor" <nate(a)bx.psu.edu> wrote:
Modi, Amit wrote:
> 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.
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.
> Thanks a lot.
> Amit Modi
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