Chris Cole wrote:
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
Hi Chris, Chances are, the files in /homes/pschofield/data/TOH are not writable by Galaxy. Galaxy was trying to convert newlines to UNIX on those files as part of the import process. This behavior was not intentional. I've just committed 3517:0c9e154e9176, which will prevent Galaxy from ever attempting to modify the import files. When copying in to Galaxy, they will still converted, but no longer "in-place" (a temp file is used). When not copying (i.e. symlinking), no newline conversion will be performed since doing so would require modifying the import file. --nate
Thanks for help.
Chris