Got this when trying CIRCSTER on latest galaxy-dist.
Does this mean my system does not know about certain genomes? Trackster works fine...
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: argument of type 'NoneType' is not iterable URL: http://srv151/visualization/circster?dataset_id=241d84796a24640a&hda_ldd... 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 galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:748 in circster view
chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey )
Module galaxy.visualization.genomes:210 in chroms view
dbkey_owner, dbkey = decode_dbkey( dbkey )
Module galaxy.visualization.genomes:24 in decode_dbkey view
if ':' in dbkey:
TypeError: argument of type 'NoneType' is not iterable
To follow up... My data file had a build key assigned to it:
Tool: BAM to BigWig Name: BAM to BigWig on data 31 Created: Jan 04, 2013 Filesize: 39.9 MB Dbkey: hg19-decoy Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 0 Full Path: /mnt/ngs/analysis/svcgalaxy/DATA/files/002/dataset_2166.dat
and my build.txt file has that build listed:
#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn ? unspecified (?) hg19-decoy Human hg19 + Decoy (BROAD; [0-9XYMT]*) (hg19-decoy) hg19-broad Human hg19 (BROAD; [0-9XYMT]*) (hg19-broad) hg19 Human hg19 (UCSC; chr[0-9XYM]*) (hg19)
On Jan 03, 2013, at 04:48 PM, Anthonius deBoer thondeboer@me.com wrote:
Got this when trying CIRCSTER on latest galaxy-dist.
Does this mean my system does not know about certain genomes?a Trackster works fine...
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: argument of type 'NoneType' is not iterable URL: http://srv151/visualization/circster?dataset_id=241d84796a24640a&hda_ldd... 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 galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:748 in circster view
chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey )
Module galaxy.visualization.genomes:210 in chroms view
dbkey_owner, dbkey = decode_dbkey( dbkey )
Module galaxy.visualization.genomes:24 in decode_dbkey view
if ':' in dbkey:
TypeError: argument of type 'NoneType' is not iterable ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Good catch; fixed in -central changeset 8d7d70348e52
Thanks, J.
On Jan 3, 2013, at 7:50 PM, Anthonius deBoer wrote:
To follow up... My data file had a build key assigned to it:
Tool: BAM to BigWig Name: BAM to BigWig on data 31 Created: Jan 04, 2013 Filesize: 39.9 MB Dbkey: hg19-decoy Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 0 Full Path: /mnt/ngs/analysis/svcgalaxy/DATA/files/002/dataset_2166.dat
and my build.txt file has that build listed:
#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn ? unspecified (?) hg19-decoy Human hg19 + Decoy (BROAD; [0-9XYMT]*) (hg19-decoy) hg19-broad Human hg19 (BROAD; [0-9XYMT]*) (hg19-broad) hg19 Human hg19 (UCSC; chr[0-9XYM]*) (hg19)
On Jan 03, 2013, at 04:48 PM, Anthonius deBoer thondeboer@me.com wrote:
Got this when trying CIRCSTER on latest galaxy-dist.
Does this mean my system does not know about certain genomes?a Trackster works fine...
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: argument of type 'NoneType' is not iterable URL: http://srv151/visualization/circster?dataset_id=241d84796a24640a&hda_ldd... 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 galaxy.web.framework.middleware.remoteuser:91 in __call__ view
return self.app( environ, start_response )
Module paste.httpexceptions:632 in __call__ view
return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.visualization:748 in circster view
chroms_info = self.app.genomes.chroms( trans, dbkey=dbkey )
Module galaxy.visualization.genomes:210 in chroms view
dbkey_owner, dbkey = decode_dbkey( dbkey )
Module galaxy.visualization.genomes:24 in decode_dbkey view
if ':' in dbkey:
TypeError: argument of type 'NoneType' is not iterable ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
-
Anthonius deBoer -
Jeremy Goecks