This is a follow-up question to the topic I had asked last week here:
As per the guidelines by @jennaj in that topic, I started with a fresh install of Galaxy and enabled access to reference genomes and indexes via CVMFS. I can now access reference genomes and indexes for almost all tools except that twobit does not show the hg38 genome (for the tool “Translate BED transcripts”) in the dropdown options.
I looked at data tables and looked in to the twobit folder and I see hg19 only for human plus the number of options are also quite less (~47 entries). Is this related to the CVMFS cache size (set at 500)? Should I be seeing a lot more options in the twobit folder?
For pursuing the second option where I use the data manager to add the hg38 index, should I follow the order?
Sam fasta index builder
Picard fasta index builder
2bit index builder
Should I source the genome from UCSC?
I just want to confirm that it will not interfere with any of the indexes sourced from CVMFS? Are there any additional things I should keep in mind before I start the indexing?