On 09/03/10 15:42, Chris Cole wrote:
On 09/03/10 14:53, Nate Coraor wrote:
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.
Ah, right. That's not clear in the docs.
How come it works with locally symlinked files, then?
Just checked it again (sorry I shouldn't have sent the previous email) with a directory and it still isn't working. www-galaxy@ge-002: tmp> cd ~/data_import/ www-galaxy@ge-002: data_import> ls README www-galaxy@ge-002: data_import> ln -s /homes/pschofield/data/TOH www-galaxy@ge-002: data_import> ls TOH/ 0min_1.txt 30m_1.txt 60min_1.txt Cd_inuc_1.txt Cmono_1.txt Dd_inuc_1.txt Dmono_1.txt processed 0min_2.txt 30m_2.txt 60min_2.txt Cd_inuc_2.txt Cmono_2.txt Dd_inuc_2.txt Dmono_2.txt www-galaxy@ge-002: data_import> ls -l total 96 -rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README lrwxrwxrwx 1 www-galaxy barton 26 Mar 9 15:59 TOH -> /homes/pschofield/data/TOH I got the TOH option in the 'Upload directory of files', which I selected, but the upload failed. Again, this is the error I get when selecting one of the filenames in the dataset: 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 Thanks for help. Chris