I've not run a stand-alone version of Galaxy, nor a cloud-based one, at present. However, I have a reference file that I wish to use to BLAST some sRNA libraries against...and know from experience that this takes a long time to do under normal operating procedure.
I am curious about whether the package for cloud based Galaxy comes standard with BLAST+? If so, can this be parallelized, as can the Desktop package? And if so...how many nodes can be supported?
Also, the documentation for the tool mentions a 'blast_datatypes' repository, and references the NCBI nucleotide/protein databases. It would seem that this is in reference to the most up-to-date collection of sequences on NCBI that one can download, and that it must be done by the user. However, if that were the case, I don't see why the need for anything outside of BLAST+ (and wrappers for it to run on Galaxy), as one would treat these as any other subset of sequences they desired to make a database to BLAST against, using the 'makeblastdb' command...no? I will, at a later point, likely want to perform BLASTs against the most recent nucleotide collection.
Thanks for your assistance!