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). Cheers, Chris