Question about the UCSC external viewer

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Question about the UCSC external viewer

Malcolm Tobias

All,

Let me try this again. My previous attempts have been bouncing.

I've succeeded in getting in getting the "display at UCSC main" link to display, but I'm getting a strange error when I'm redirected to the page. I can't cut-and-paste the error, so hopefully the attached screen shot wont get eaten by the mailing list.

From the galaxy log, I'm seeing the UCSC viewer request data:

128.114.119.133 - - [13/Jun/2013:08:47:22 -0500] "GET /display_application/6505e875ddb66fd2/ucsc_bam/main/None/data/galaxy_6505e875ddb66fd2.bam HTTP/1.0" 200 1130428 "-" "genome.ucsc.edu/net.c"

but I don't see anything like "6505e875ddb66fd2" under display applications:

[galaxy@login002 ~]$ ls -l galaxy-dist/display_applications/

total 48

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 ensembl

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 gbrowse

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 igb

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 igv

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 rviewer

drwxr-xr-x 2 galaxy galaxy 8192 May 15 12:12 ucsc

While the UCSC viewer is requesing data from the "display_application" subdirectory, I only have a "display_applications" subdirectory. I'm not seeing anything like "6505e875ddb66fd2" under galaxy-dist, so maybe I'm not doing some pre-processing needed before being redirected to UCSC?

[galaxy@login002 ~]$ find galaxy-dist -name '*6505*' -print

[galaxy@login002 ~]$

Any suggestions on what might be going wrong?

Cheers,

Malcolm

--

Malcolm Tobias

314.362.1594


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

login2.png (12K) Download Attachment