So we did the following: Downloaded the data Added the paths to .loc file restarted galaxy

We still are getting the following error:

2: Extract Genomic DNA on data 1 empty format: fasta, database: hg19 56 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 56 invalid lines, 1st is #1, "chr22 23487552 23487738 NM_004914_cds_0_0_chr22_23487553_f 0 +"

My guess is that you .loc file is not set up correctly; you'll need to make sure that there are tab characters—not spaces—separating the columns. If that's not the case, try finding the command line in the galaxy log and running it from the command line (make sure to prepend the command with 'PYTHONPATH=./lib' to get needed Galaxy libraries) and adding debugging statements to see why you twobit file isn't being found. Line 200 of extract_genomic_dna.py may be the key failure point. Finally, please keep all replies on the mailing list for community purposes. Thanks, J.