HISAT2 index builder requirements



I’m using my own local Galaxy (release 18.09), and I’m trying to add hg38 genome assembly on HISAT2. I’m managing that from data manager in the Admin section, and I installed the last available versions of HISAT2 index and HISAT2. When I used HISAT2 index builder for getting hg38 an error occurred.

I checked for the HISAT2 index builder dependencies and it requires the 2.0.5 version of HISAT2, that isn’t available on galaxy, hence the dependency can’t be resolved. Is it possible that the unsolved dependencies are causing the issue?
Maria Paola


The DM is installing its dependencies from bioconda, which should have hisat 2.0.5 so this is probably a different problem. It seems the DM is unable to find the proper directory but looking at the code it should be creating it…

 target_directory = params[ 'output_data' ][0]['extra_files_path']
    if not os.path.exists( target_directory ):
        os.mkdir( target_directory )


Thanks for your help. I think it is starting the uploading because the job takes space on the disk and the error occurs only at the end. Do you have any suggestions?