I am using Tophat in Galaxy (Galaxy version 0.9). In TopHat tool’s setup menu in Galaxy, there is an option: “Use a built in reference genome or own from your history”, and this option has two choices: “Use a built-in genome” and “Use a genome from history”. When I choose “Use a genome from history”, I can provide Tophat with my reference genome fasta file in my workflow.
However, this means that every time when Tophat runs, it first builds bowtie2 index files on-the-fly from the reference genome fasta file I provided. This slows down the process a lot, and also has “insufficient memory” problem (bowtie2-build aborted) when I run Tophat twice for two fastq samples in one workflow.
So I am wondering if there is a way to specify our pre-built bowtie2 index files when running Tophat in Galaxy, so that I can just use them in multiple Tophat runs in my workflow without having to build them on-the-fly in each Tophat run. I searched through the TopHat tool’s setup menu in Galaxy but could not find this kind of option.
So, is there a way to store our pre-built bowtie2 index files in database and make them “a built-in genome”? If so, what are the required steps for doing that?
Since I need to use different annotations for different workflows, I am also wondering if we can have multiple “built-in genome” for the same organism?
I would greatly appreciate any help on this problem.
Thank you very much!