Galaxy local instance - need for FTP?

Question: Galaxy local instance - need for FTP?

2.4 years ago by

balaszone • 60 wrote:

Hello,

I know this is a common question but I don't find a very specific answer to my question in the forum. I hope somebody could help.

I successfully installed local instance galaxy in our server. We have huge data sets (about ~100GB each) that we need to process. Obviously I was not able to upload this into galaxy webserver which is limited to just 2GB. It recommends me to upload via a FTP server. My question is, can't I just keep my data in my own server(where galaxy is also installed) and process right there? I dont see why I need to use FTP to upload and then process the data. Could somebody guide me on this? Maybe I didn't understand the purpose of local instance?

Thanks much in advance, B

local instance ftp cloud • 849 views

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modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by balaszone • 60

2.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These are the instructions for loading local data into a local Galaxy: https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

That was helpful. Thanks. My follow up question is - when using data libraries, if I'm only accessing my original data via symbolic links, where will the processed output be placed? In other words, say if my original data is in FASTQ format and I convert it in galaxy to BAM format. Where will the BAM files be placed, especially given the HUGE size of my FASTQ file(~100GB). In other words, where will the output data be placed after each analysis step? Could you please clarify this?

Thanks, B

ADD REPLY • link written 2.4 years ago by balaszone • 60

Hi B,

The data would start off being loaded into a Data Library. From there, it is moved into a History to work with it. Result datasets in Histories are within the Galaxy file system.

This is the same as all Galaxy analysis - except in your case the datasets are loaded into the working History from a Data Library, instead adding them in with a Get Data tool, the Upload tool, another shared object (Dataset or History from a Page), etcetera.

Please let us know if this does not help enough. - Jen

ADD REPLY • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you.

Just to clarify - So once it is loaded into Galaxy history, all the data and the results of analysis are physically sitting and occupying space in the galaxy server? Is that right?

Thanks!

ADD REPLY • link written 2.4 years ago by balaszone • 60

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