Weird problem with importing datasets
Hi, I've enabled the 'library_import_dir' option in universe_wsgi.ini as: library_import_dir = /homes/www-galaxy/data_import It's contents is: www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 40 Mar 4 14:40 Dd_inuc_1.txt -> /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README However, both files fail to import with this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error The strangeness comes in if I copy to the Dd_inuc_1.txt file a directory owned by the www-galaxy user and link to it there. Then, the imports works for both files. www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 20 Mar 5 13:56 Dd_inuc_1.txt -> ../tmp/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README The permissions are correct for the file: www-galaxy@ge-004: data_import> ls -l /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 pschofield barton 966480362 Jan 18 16:39 /homes/pschofield/data/TOH/Dd_inuc_1.txt I've no idea why Galaxy cares about who owns the files as it should be able to see them, but something's screwy. Anyone have ideas as to what's going on here? Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
Anyone got any ideas on this? It's still not working (following the most recent updates) and we've got some NGS data to import into Galaxy. Also, it isn't honouring the 'Copy data into Galaxy?' when I set it to 'No'. I moved the file and yet I can still use it for further analysis. Any help is much appreciated. Thanks, Chris On 03/05/2010 02:06 PM, Chris Cole wrote:
Hi,
I've enabled the 'library_import_dir' option in universe_wsgi.ini as: library_import_dir = /homes/www-galaxy/data_import
It's contents is:
www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 40 Mar 4 14:40 Dd_inuc_1.txt -> /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README
However, both files fail to import with this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error
The strangeness comes in if I copy to the Dd_inuc_1.txt file a directory owned by the www-galaxy user and link to it there. Then, the imports works for both files.
www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 20 Mar 5 13:56 Dd_inuc_1.txt -> ../tmp/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README
The permissions are correct for the file: www-galaxy@ge-004: data_import> ls -l /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 pschofield barton 966480362 Jan 18 16:39 /homes/pschofield/data/TOH/Dd_inuc_1.txt
I've no idea why Galaxy cares about who owns the files as it should be able to see them, but something's screwy. Anyone have ideas as to what's going on here? Cheers,
Chris
Chris Cole wrote:
Anyone got any ideas on this?
It's still not working (following the most recent updates) and we've got some NGS data to import into Galaxy.
Hi Chris, To use this feature, the contents of library_import_dir should themselves be directories (or symlinks to the same). Selecting that directory from the dropdown in the library upload form will then import the contents of those directories. --nate
Also, it isn't honouring the 'Copy data into Galaxy?' when I set it to 'No'. I moved the file and yet I can still use it for further analysis.
I'll have a look at this.
Any help is much appreciated. Thanks,
Chris
On 03/05/2010 02:06 PM, Chris Cole wrote:
Hi,
I've enabled the 'library_import_dir' option in universe_wsgi.ini as: library_import_dir = /homes/www-galaxy/data_import
It's contents is:
www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 40 Mar 4 14:40 Dd_inuc_1.txt -> /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README
However, both files fail to import with this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 326, in __main__() File "/homes/www-galaxy/galaxy_devel/tools/data_source/upload.py", line 318, in __main__ add_file( dataset, error
The strangeness comes in if I copy to the Dd_inuc_1.txt file a directory owned by the www-galaxy user and link to it there. Then, the imports works for both files.
www-galaxy@ge-004: data_import> ls -l total 96 lrwxrwxrwx 1 www-galaxy barton 20 Mar 5 13:56 Dd_inuc_1.txt -> ../tmp/Dd_inuc_1.txt -rw-r--r-- 1 www-galaxy barton 142 Mar 5 13:50 README
The permissions are correct for the file: www-galaxy@ge-004: data_import> ls -l /homes/pschofield/data/TOH/Dd_inuc_1.txt -rw-r--r-- 1 pschofield barton 966480362 Jan 18 16:39 /homes/pschofield/data/TOH/Dd_inuc_1.txt
I've no idea why Galaxy cares about who owns the files as it should be able to see them, but something's screwy. Anyone have ideas as to what's going on here? Cheers,
Chris
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Nate Coraor wrote:
Also, it isn't honouring the 'Copy data into Galaxy?' when I set it to 'No'. I moved the file and yet I can still use it for further analysis.
I'll have a look at this.
I can't recreate this. When you move the file, it should no longer be accessible via the 'eye' or 'save' links. It will still appear in libraries and histories, though, since this metadata is stored in Galaxy and no check is performed to see whether the disk file has been removed. Can you check and determine whether this is the case? Thanks, --nate
On 09/03/10 15:15, Nate Coraor wrote:
Nate Coraor wrote:
Also, it isn't honouring the 'Copy data into Galaxy?' when I set it to 'No'. I moved the file and yet I can still use it for further analysis.
I'll have a look at this.
I can't recreate this. When you move the file, it should no longer be accessible via the 'eye' or 'save' links. It will still appear in libraries and histories, though, since this metadata is stored in Galaxy and no check is performed to see whether the disk file has been removed. Can you check and determine whether this is the case?
Ah, yes. The eye and save links don't work. I must have been doing something wrong, I can't remember exactly as it was a couple of days ago. Thanks, Chris
participants (2)
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Chris Cole -
Nate Coraor