How to load BAM from remote computer

[Amy]

Hello!

I am trying to load BAM files found on my home institution's computing cluster. What would be the best way to access BAM files on a remote computing cluster if I were to do this relatively frequently and the BAMs may be stored along different subdirectories of the same filesystem?

1. My local installation of IGV is 2.11.4 on macOS Big Sur 11.6.

2. I was advised by a colleague to try using "File > Load from URL..." but came across a "File not found" error immediately after submitting the URLs for the BAM and corresponding BAI (in same directory). I was expecting a password prompt but did not receive that -- only the error message, which occurred immediately. I initially formatted the URLs the same way I would for using the rsync command in Terminal but have also tried other sensible formats (e.g. including the "sftp" heading) and checked that I am on my institution's WiFi network (in case it was a firewall issue).

HOWEVER, I am not committed to using the "File > Load from URL..." functionality if there is a method better suited for my needs.

3. I have attached the igv.log, but it does not specifically show my error, which I have recreated just now and should be the final entry in the log. Since the error does not seem to be specified in the log, I am also attaching a screenshot of the error-message window.

Thank you,

Amy

[James Robinson]

Hi, IGV is not designed for this use case, it is a desktop application.  if you cannot access the files through the File dialog from the menu I do not know anyway to access them.    The "URL" solution could work if your institution makes them available that way, i.e. serves them from an http server.   You will need to work with your home institution to find a solution.