Cristian,

You can use your FASTA file with the NGS mappers (BWA, Bowtie, Lastz). Galaxy allows you to upload a gzipped file into your history, which it extracts after you upload it. Note that the file should be a single FASTA file containing all chromosomes/scaffolds/etc., each marked with a single header line. (Also, the file can only be gzipped (not tarred and gzipped)--it looks like yours is fine.) Then, when you are going to do the mapping, select the Use one from your history option instead of using one of the built-in indexes. Galaxy will create the indexes that the mapper needs from your supplied FASTA file before it does the mapping. 

Let us know if you need any further assistance.

Regards,

Kelly