FTP and command line access in Galaxy
Nate, The Galaxy's ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? If not, would it be easy to add? Regards, Curtis
Hi Nate,
We'd like to set up our local Galaxy to be able to import data (fastq
sequences) from an ftp site (with a username/password) into a user's
account. Does Galaxy support FTP or would we have to write a wrapper
script to do it via HTTP and use the standard data connection methods as
described in http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources?
Hi Steve,
You can actually put FTP URLs directly in the URL/paste box on the
upload form. With a username and password, the format would be:
ftp://user:pass@example.org/path/to/file.ext
I haven't tested that the user/pass bit works, but it should.
Yep. It works. Thanks for the tip!
On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson <curtish@uab.edu> wrote:
Nate,
The Galaxy’s ability to pull files with user/password from FTP sites as a client is great.
However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this?
Try asking the sequencing centre if the username and password can be provided as part of the HTTP URL, then give that URL to Galaxy. Peter
Peter Cock wrote:
On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson <curtish@uab.edu> wrote:
Nate,
The Galaxy’s ability to pull files with user/password from FTP sites as a client is great.
However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this?
Try asking the sequencing centre if the username and password can be provided as part of the HTTP URL, then give that URL to Galaxy.
If it's using HTTP Authentication, the URL is the same as with ftp: http://user:host@example.org/file.ext Other authentication systems which use forms and cookies or similar methods won't work. --nate
Peter
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participants (3)
-
Nate Coraor -
Peter Cock -
Robert Curtis Hendrickson