Loading from username/password protected ftp

[tom carroll]

Dear list,

I am trying to test loading a file from Broad FTP using load URL in IGV. 

The file requires a username to log in so if I provide the username in the URL I can download from a browser. 

Link to file : -" ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle//hg18/1000G_omni2.5.hg18.vcf.gz"

I am not sure how and how best to load a username/password protected file into IGV with a URL?

If I try posting "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle//hg18/1000G_omni2.5.hg18.vcf.gz" in the load url box, I am asked by text box to enter a username and password. Here entering the "gsapubftp-anonymous" as username and password as blank does not work.

When I simply try and load the ftp URL directly "ftp://ftp.broadinstitute.org/bundle//hg18/1000G_omni2.5.hg18.vcf.gz" the text box asking for username and password doesn't appear.

I understand this data may be available by the "load from server" method but I was wondering what is the best practice to load from password protected ftp?  I thought the Broad FTP should be a good example for my question.

The example of loading from Apache server worked perfectly with entering username and password into the text box allowed IGV to retrieve file.

Thank you for all your work on IGV and for any help here,

tom

[James Robinson]

Hi,

First loading indexed files by FTP is unreliable and no longer supported,  FTP access has not been supported for some time.   The code is still there, and it might sometimes work anyway, but it's not recommended.

Your syntax is correct, but that URL does not require a password so the popup dialog does not appear.   It successfully connects and dies later in the htsjdk trying to decompress the first bgzip block. 

Jim

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[tom carroll]

hi Jim,

Thank you for the reply and clarification.

best,

tom

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[James Robinson]

Sorry I couldn't be more helpful,  hopefully you can use http or https for your purposes.   I think there is an open issue on the htsjdk project about FTP issues but I would not expect rapid action on it.

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