I got a local instance of galaxy on my computer, and wanted to run a differential expression analysis for some samples of human RNA-seq data. I’ve managed to download the fastq reads for the samples and I’ve downloaded and indexed the human genome using HISAT2 index builder. But when I tried to align the reads from just one of the six files, it wasn’t able to align them in almost 60 hours of running. So I decided that I’d need to do this on the cloud. However, I don’t want to have to reinstall the tools, and re-download all the files and re-index the genome. I was wondering if there was any way to take whatever I have on my computer, and put it onto the cloud as is, so that I can pick up where I left off.
It’s not possible to transfer a local setup to CloudMan/GVL and instead the tools would needs to be installed again. The GVL does come with a number of tools pre-installed, so perhaps the tools are already available, or maybe only a couple of them would need to be installed. It also comes with a bunch of reference data so hopefully that would not need to be setup.
An alternative you could perhaps try is to use the GalaxyCloudRunner: https://galaxycloudrunner.readthedocs.io/en/latest/
This is still under development (you would likely be the first user), but in principle, it allows you to connect additional cloud machines to your local Galaxy instance. The remote instance will generally be automatically setup for the necessary tools at runtime while it’ll transfer the data automatically.
In theory, yes, however, the history export/import functionality isn’t yet quite as wonderful as we would like it to be. This is an active priority for us to improve.
But you could try and see how it works with your given history’s data content
