Question

Bam Viewer That Works On Authenticated Ftp Urls With Username/Password Combination?

1

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12.5 years ago

Biostar User ▴ 360

Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination?

For example, something like this:

~/myfavouritebamviewer view ftp://username:password@my.ftp.site/file.bam

next-gen bam software • 2.1k views

ADD COMMENT • link updated 12.5 years ago by Istvan Albert 102k • written 12.5 years ago by Biostar User ▴ 360

0

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you could try to mount this site as a directory with FUSE, then any viewer will treat files within as normal files

ADD REPLY • link 12.5 years ago by Jeremy Leipzig 22k

score 1 · Answer 1 · 2012-06-14

Integrative Genomics Viewer (IGV) works with http sites that require authorization, I think it will work with FTP, a quick test indicates that it can connect, and most network libraries can handle http as well as ftp. That being said the FTP protocol is a lot trickier than HTTP as it has multiple modes of operation: active/passive plus other things. So this will also depend on the server settings.

(You may need to specify the username and/or password in the url, ouch!)