On 12/04/10 22:26, Nate Coraor wrote:
Chris Cole wrote:
Sorry for the delay, only just got back to looking at this.
Following the latest updates (tip is now 3560:4c95f1a101f1) I can now successfully update files not belonging to Galaxy. However, softlinks in the import directory aren't being dereferenced correctly.
e.g. This is the contents of the import directory: caterpillar: /homes/www-galaxy/data_import> ls -l total 96 -rw-r--r-- 1 www-galaxy barton 142 Mar 9 14:14 README lrwxrwxrwx 1 ccole barton 65 Mar 25 15:47 solexa_files -> /homes/ccole/projects/Dicty_RNAseq/raw_data/NOBACK/SOLEXA results
I deleted the softlink following upload, but now the files are no longer accessible. FASTQ Groomer for example reports this error: Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 37, in ? if __name__ == "__main__": main() File "/homes/www-galaxy/galaxy_devel/tools/fastq/fastq_groomer.py", line 18, in main for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): IOError: [Errno 2] No such file or directory: '/homes/www-galaxy/data_import/solexa_files/Ax2.txt'
So, it looks like Galaxy didn't dereference the 'solexa_files' softlink (to me at least).
Hi Chris,
This wasn't part of the original design. We were handling when the contents of import directories were symlinks, but not when the import directories themselves were symlinks. This has been added in 3629:6b93e705c8a4.
Oh, right. I got the impression that all the symlinks were dereferenced once. Thanks for the update. I'll check it out when it gets to the main tree. Thanks again for your help. Cheers, Chris