Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Uploading multiple FastQ files from BaseSpace to Galaxy
0
gravatar for gkuffel22
3.7 years ago by
gkuffel22 • 170
United States
gkuffel22 • 170 wrote:

Hi,

Hoping someone can help. I have a run that recently completed on our Illumina MiSeq and the FastQ files are on BaseSpace. I am able to generate a URL for this project containing these files. Is there a way to use FTP (Cyberduck) to send all of these files to the main instance of Galaxy using this generated URL so that I do not have upload each file separately (there are 150 files). Thanks for the help.
basespace ftp galaxy • 2.5k views
ADD COMMENT • link •
modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by gkuffel22 • 170
0
gravatar for Martin Čech
3.7 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

If you have an ftp address for the file you can simply have Galaxy fetch it through the upload modal. See the screenshot: https://www.dropbox.com/s/7nvq35ef7qo1kug/Screenshot%202015-03-30%2013.58.22.png?dl=0
ADD COMMENT • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

I do not have a ftp address, I simply have a URL generated by basespace for sharing purposes:  http://basespace.illumina.com/s/project#. 

ADD REPLY • link written 3.7 years ago by gkuffel22 • 170

I have created a BaseSpace account and tried to explore the UI a bit and it seems this is not easy as Illumina does not provide any raw sharing of your data unless you use the API.

You can explore the following links on how to use the API and get your data programatically but Illumina does not provide you with FTP server or sharing links that you could connect to from Galaxy.

https://github.com/nh13/basespace-invaders
http://dskernel.blogspot.com/2012/11/fetching-data-from-illumina-basespace.html
https://www.biostars.org/p/117567/
http://www.homolog.us/blogs/blog/2014/11/26/downloading-basespace-files-using-command-line/
 

EDIT: This might allow you to obtain url that Galaxy can use to fetch the data for you: 

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by Martin Čech ♦♦ 4.9k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour