Question: 403 Forbidden Uploading Data from S3 in Galaxy
1
gravatar for Blayze Stefaniak
7 days ago by
Blayze Stefaniak10 wrote:

I created a custom Galaxy implementation given the following instructions: https://galaxyproject.org/cloudman/

I am receiving 403 forbidden errors when navigating to Get Data > Upload File > fastq > Homo sapiens > paste in the textbox something resembling this URL: https://s3.amazonaws.com/example-bucket/fastq/example-read1.fastq

Per this discussion below, I edited my bucket_default environment variable in the user-data, and validated that my user has full s3 access in AWS IAM: https://biostar.usegalaxy.org/p/13099/

I've tried logging in as admin at https://galaxy.example.com/cloud as well as subscribing and logging in as an individual with my email. Neither approach worked as expected and cleared the 403 error. I tried making it s3://example-bucket/fastq/example-read1.fastq however it just uploads this as text.

Is there something obvious I am missing? Is there any documentation for how to access this file, perhaps it explains how to pass AWS credentials?

Thank you, Blayze

ADD COMMENTlink modified 6 days ago • written 7 days ago by Blayze Stefaniak10

Thank you for the insight as this seems to highlight the root cause. However, I am not going to make my organization's PHI publicly accessible.

ADD REPLYlink written 6 days ago by Blayze Stefaniak10

You may want to look into generating a pre-signed download URL for those particular datasets as an alternative to making them public

ADD REPLYlink written 6 days ago by Dannon Baker3.6k
2
gravatar for Enis Afgan
7 days ago by
Enis Afgan440
United States
Enis Afgan440 wrote:

It sounds like there are two concepts being mixed up a bit here. The bucket_default bit is all stuff related to CloudMan and is hence not relevant when just uploading data to Galaxy. To log into the CloudMan console, use username ubuntu and the password you supplied when launching the instance.

To get data into Galaxy from S3 (or any other public URL), you should choose Get Data ā†’ Upload File ā†’ Paste/Fetch data (button at the bottom of the overlay) ā†’ paste in the URL. They key portion of this process is that the data at the provided URL is publicly available. You can check if that's the case by pasting the URL in your browser address bar and the file should start downloading. If it's not, for S3, you'll need to make the file public from within the AWS S3 web console.

These two screenshots capture what I described:

enter image description here

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ADD COMMENTlink written 7 days ago by Enis Afgan440
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