I am a fairly new administrator for a Galaxy Server in a Biomedical company. My users informed me we have a genome called hg38 loaded into Galaxy in such a way that the users are unable to run BWA_MEM for hg38 ending with a message saying it was unable to locate the index files. They have asked I remove the genome entries and they will add it again in the same manor as other genomes (which all work). I have not located an obvious way to do this. Here are some details:
You can hopefully see from the image that hg38 appears to be loaded 3 times. 2 of those times are references using “/cvmfs”. All 3 use the same dbkey so I suspect the nature of the issue is related to that. When the users originally reported about the missing indexes there were only two loaded and both were “/cvmfs”. Since reporting they have attempted to correct the issue themselves by reloading using the local file system, hence now 3 entries.
Its installed on Ubuntu 18.04.2 LTS. I’m reasonably confident this is for Galaxy version 19.09 but I’m not sure how to tell confidently so I used the “git log” command in the installation directory and all the top entries are for 19.09. The install was done on 26Jan2020 by me. I did not know at the time I should record the version on the welcome page. Appreciate any thoughts or pointers to documentation steps to remove a genome. Cheers.