I have previously used the NCBI accession download tool and NCBI Datasets Genomes as well as Faster Download and Extract Reads in FASTQ. But I am not able to retrieve it from the NCBI database.
Accession number: GCA_000863945.2.
Seeing your follow-up post on bwa and igv, I assume you’ve solved this problem here?
No, I manually downloaded the genomic assembly from NCBI and uploaded it. Is it possible to retrieve the data directly from NCBI to Galaxy Europe using a retrieving tool?
The simplest solution is to go to the ftp tab at Human papillomavirus 16 genome assembly ViralProj15505 - NCBI - NLM, then right-click the file you want and copy the link to it.
In the upload dialogue in Galaxy you then go to Paste/Fetch data and paste the copied link into the text area. Press start and your upload should start running.
If your browser has issues displaying the NCBI FTP site, you can use the NCBI Datasets Genomes tool. I just tried with your data and it’s working for me.