Ftp And Command Line Access In Galaxy

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Question: Ftp And Command Line Access In Galaxy

8.7 years ago by

S Taylor • 20

S Taylor • 20 wrote:

Hi, 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? My next question is, are there any recommendations to make it possible to allow access to Galaxy imported and generated data to be processed outside of Galaxy e.g. via command line? I guess using sudo and cp is an option but I wondered if anyone had any more thoughts on this! Thanks for any advice, Steve

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modified 8.7 years ago by Nate Coraor ♦ 3.2k • written 8.7 years ago by S Taylor • 20

8.7 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

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. There's nothing at present, although an API should soon be in the works that will make writing scripts for such things simpler. --nate

ADD COMMENT • link written 8.7 years ago by Nate Coraor ♦ 3.2k

Hi Nate, Yep. It works. Thanks for the tip! Is there any design docs for for this to give an idea of what the plans are? Thanks, Steve

ADD REPLY • link written 8.7 years ago by Steve Taylor • 240

Not really. It'll be RESTful, but beyond that very little has been thought about.

ADD REPLY • link written 8.7 years ago by Nate Coraor ♦ 3.2k

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