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
S Taylor 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?
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.
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!
There's nothing at present, although an API should soon be in the works that will make writing scripts for such things simpler. --nate
Thanks for any advice,
Steve
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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!
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!
There's nothing at present, although an API should soon be in the works that will make writing scripts for such things simpler.
Is there any design docs for for this to give an idea of what the plans are? Thanks, Steve
Steve Taylor wrote:
There's nothing at present, although an API should soon be in the works that will make writing scripts for such things simpler.
Is there any design docs for for this to give an idea of what the plans are?
Not really. It'll be RESTful, but beyond that very little has been thought about.
participants (3)
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Nate Coraor -
S Taylor -
Steve Taylor