Load from URL using SMB link

[Cody Ramirez]

Is there a way to load a BAM file using a SMB link?

[Helga Thorvaldsdottir]

Hi - Are you on a Mac? Once you've mounted a drive, you can load a file on that drive through the File > Load from File menu (not from URL), and use the file browser to go to your <computer_name>. You'll probably see the mounted disk there, but if not you can find it under "Network", and then navigate down to the file as with any other file on your system.  I just verified this in IGV 2.9.4 on Catalina.

[Cody Ramirez]

Thank you so much. I found it, I thought I would be able to just copy and paste the samba link. Clicking, mounting and navigating to the file worked for me too. Thank you so much.

[Arnaud Ceol]

Hi,  I have the same problema as Cody.

What I'm trying to do is share an IGB sessions with colleagues in my institute. The files are on a smb/cifs share (important because we need authentication to access those files). The idea was therefore to insert the smb://path url (instead of https or a local path). Nevertheless  the smb URL is interpreted by IGV ad a local path :  /User/userID/smb:/path , and therefore IGV fails to load the session.

Thanks in advance to anyone who can help.

Arnaud

[James Robinson]

Hi Arnaud,

I don't understand what you mean by "the smb URL is interpreted by IGV as a local path...".   Where are you entering an smb URL?  

Jim

[Arnaud Ceol]

Sorry, I dropped this conversation a long time ago. I'm still strugling with it. To summarize:

- I can mount a smb volume and access the files from IGB but I would not be able to share the session with others (different path). What I would lie to do is access directly from a smb:// url.

- If I fill the "load from url" , with a smb://myurl , the error message is File not found: smb://myurl

- if I modify a session and insert "<Resource path="smb://myrul">..." the error message will be " Errors were encountered loading the session:
/Users/username/smb:/myurl
  org.broad.igv.exceptions.DataLoadException: /Users/username/smb:/myurl (No such file or directory)

I guess it means that IGV does not accept smb urls. Thsi would be really useful, because it would help us providing access to the files in a genome viewer while preserving file permissions at the posix/acs level of the file system.

[igv-help]

First I assume you mean "IGV", but if you really intended to ask a question about "IGB" that is another project.

You are correct, SMB urls are not supported.   That would be difficult for us to take on, not least because we do not have any SMB servers.   We would entertain a pull request,  but should have some discussion first.  The best place for discussions like this is our github site,  https://github.com/igvteam/igv/issues.

-- Jim