Want to use reference Genome hg19 for Bowtie2 from a local instance of Galaxy. The pulldown for selecting a reference genome index has none. My local shared libraries pulldown is also empty. The online version has them. How do I get this data into my local session? Or am I supposed to be able to see the the databases online?
You can fetch genome using the tool data_manager_fetch_genome_all_fasta . After you find this tool in the tool shed and install to the local Galaxy instance, go to Admin -> Data -> Local Data . Then under Run Data Manager Tools, you'll see Reference Genome. You can then use it to download genome into local instance of Galaxy.
For Bowtie2, you'll also have to index the genome first. After you get the genome, install data_manager_bowtie2_index_builder . Then again under Run Data Manager Tools, you can build Bowtie2 index for the genome you installed.