OK (I see now I have posted twice the same error from the log - silly of me, sorry).

First this: yes, the permissions in the data library are set so that only I and one other person can access the data library (set by one sharing role for both of us)


The entries in the job table related to the summary tree converter:

--
select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc;
--




id | create_time | update_time | history_id | tool_id | tool_version | state |
info |
command_line
| param_filename | runner_name |
 stdout | stderr | traceback | s
ession_id | job_runner_name | job_runner_external_id | library_folder_id | user_id | imported | object_store_id | params | handler | exit_code
------+----------------------------+----------------------------+------------+--------------------------------------+--------------+-------+-----------
----------------------------------------------------------------------------------------+--------------------------------------------------------------
-------------------------------------------------------------------------------------------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------------------------+----------------+-------------+
--------+-------------------------------------------------------------------------------------------------------------------------------+-----------+--
----------+-----------------+------------------------+-------------------+---------+----------+-----------------+--------+----------+-----------
8186 | 2013-03-19 09:22:29.165135 | 2013-03-19 09:27:44.335526 | 622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok |
| python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte
rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10477.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1481.dat /m
nt/galaxydb/files/013/dataset_13752.dat |                |             |
| |           |
6188 | local:/// | 25218 | | 1 | f | | | handler3 | 0 8185 | 2013-03-19 09:22:19.463602 | 2013-03-19 09:22:23.644461 | 622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | new |
|

|                |             |
| |           |
6188 | local:/// | | | 1 | f | | | handler2 | 8184 | 2013-03-19 09:20:45.225881 | 2013-03-19 09:26:54.337624 | 622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok |
| python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte
rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1478.dat /m
nt/galaxydb/files/013/dataset_13749.dat |                |             |
| |           |
6188 | local:/// | 25112 | | 1 | f | | | handler1 | 0 8183 | 2013-03-19 09:20:44.865602 | 2013-03-19 09:27:19.370773 | 622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok |
| python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte
rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10461.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1477.dat /m
nt/galaxydb/files/013/dataset_13750.dat |                |             |
| |           |
6188 | local:/// | 25113 | | 1 | f | | | handler1 | 0 8163 | 2013-03-19 08:29:59.965262 | 2013-03-19 08:34:30.257029 | 622 | CONVERTER_bam_to_summary_tree_0 | 1.0.0 | ok |
| python /home/galaxy/galaxy-dist/lib/galaxy/datatypes/converte
rs/sam_or_bam_to_summary_tree_converter.py --bam /mnt/galaxydb/files/010/dataset_10457.dat /mnt/galaxydb/files/_metadata_files/001/metadata_1475.dat /m
nt/galaxydb/files/013/dataset_13719.dat


Thanks,


Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 03/19/2013 10:54 PM, Jeremy Goecks wrote:
Indeed, following error occurs:

157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] "GET /visualization/trackster HTTP/1.1" 200 - 
"http://galaxy.bits.vib.be/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.22+ (KHTML, like 
Gecko) Chromium/17.0.963.56 Chrome/17.0.963.56 Safari/535.22+"
galaxy.webapps.galaxy.api.datasets ERROR 2013-03-19 08:30:13,722 Error in 
dataset API at listing contents: :
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
line 41, in show
    is_true( kwd.get( 'retry', False ) ) )
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
line 96, in _converted_datasets_state
    if not data_provider.has_data( chrom ):
  File 
"/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", 
line 814, in has_data
    st = summary_tree_from_file( self.converted_dataset.file_name )
  File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py", 
line 114, in summary_tree_from_file
    st = cPickle.load( st_file )
EOFError
This is the error that occurs when trying to read a dataset's index. What you 
want to look for is the error that occurs when creating this index; you'll need 
to look in the database to find this error. Here's a SQL command that will look 
for the most recent summary tree converter jobs:

--
select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc;
--

Is there anything in standard out/error that would explain why the summary tree 
is not created?


I have found the root cause I believe:
when I visualize datasets from a data library, the data is not displayed.
Getting them from the source history gets displayed is OK
Importing them from a data library in a history, and displaying in trackster 
works
I cannot reproduce this on a clean version of galaxy-dist. One guess is library 
permissions may be causing a problem. Are the datasets that you want to 
visualize in a library (or they themselves) under restricted access?

Thanks,
J.


___________________________________________________________
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/

Reply via email to