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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Visualization with UCSC Genome Browser #72

Open ammeyer opened 7 years ago

ammeyer commented 7 years ago

Hi all -- Getting tripped up with the step involving actually using the UCSC interface for visualizing alignments. I have successfully run hal2assemblyHub.py but am confused about what it means to make the hub.txt file addressable as a public URL. I'm sure there is an easy way to do this, maybe with a local web server? Any advice would be appreciated. Thanks Abby

joelarmstrong commented 7 years ago

Hi Abby,

Yep, to view the hub using the browser you need to make the hub files public. (You could also host your own browser locally to visualize it, but that's probably more complicated than just making the hub public.)

Most institutions provide web hosting for their employees/students. If you have access to that, making files public is typically as easy as copying them to a "public_html" directory on a server. That's what we do. But otherwise, a local web server might work, although making sure it can be reached from the Internet can be a little tricky.

This page should help explain what to do with the hub.txt URL once it's public.

Hope this helps!

ammeyer commented 7 years ago

Thank you! I will try to get my institution to help with web hosting.