I've just finished setting up a local Galaxy instance and everything works fine except for built-in reference genomes both with the "Map with BWA for Illumina" and "Map with Bowtie for Illumina" tools. I am able to use the same reference genomes without any problem if I set them up as files in the history. I first tried to set up the .loc and fasta files manually as instructed on this page:
When using the Bowtie tool, I can't see any reference genomes in the drop down menu for built-in indexes. When using the BWA tool, I see the genomes, but I get the following error right as the task starts:
The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/galaxy/data/Arabidopsis_thaliana_TAIR10/bwa_index/Arabidopsis_thaliana_TAIR10.fa.bwt'. Abort! Aborted
I thought maybe I had made a mistake in setting up the genomes, so I used rsync to copy all the .loc files and the Arabidopsis genome from the public Galaxy server, but I get exactly the same error. This is strange, considering this alignment has been completed successfully on the public server in the past, using the same dataset and the same built-in genome.
I've read in other posts that this could be a memory issue, so I tried setting up a smaller genome (less than 130 kb), and I get the same error.
I can get both of the tools to work properly using files from the history, but this would be much less convenient in the long term.
I would appreciate any ideas on what I could try next.