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.