This process requires an initial setup by Genoox
Before you could upload samples from Amazon S3 repository, please send out
a request email to [email protected] from one of the organization admins
or contact us using the embedded support wizard.
The email needs to specify the name and region of the S3 Bucket you are interested in uploading from.
Once the initial setup by Genoox support team has been completed, please follow the next steps
Open AWS S3 Service from AWS Console
Locate the bucket from which you'd like to upload data
Open the Permissions Tab
Navigate to Bucket Policy
add the following JSON (or append an object to Statement list if there is already something there):
{
"Version": "2012-10-17",
"Statement": [
{
"Effect": "Allow",
"Principal": {
"AWS": "arn:aws:iam::<GENOOX_ACCOUNT_NUMBER>:user/<GENOOX_COMPANY_UPLOADER>" },
"Action": [
"s3:GetBucketLocation",
"s3:ListBucket",
"s3:GetObject"
],
"Resource": [
"arn:aws:s3:::<COMPANY_BUKCET_NAME>",
"arn:aws:s3:::<COMPANY_BUKCET_NAME>/*"
]
}
]
}📘Make sure to modify the values from the JSON accordingly
GENOOX_ACCOUNT_NUMBER - Will be provided by the Genoox support team
GENOOX_COMPANY_UPLOADER - Will be provided by the Genoox support team - a dedicated user for your organization
COMPANY_BUKCET_NAME - The Bucket name from which the upload should occur
From the AWS Console, this how how the configuration should appear
Once you have completed the configuration - you can now add the S3 Bucket to Genoox platform and upload files or folders directly from S3
Navigate to New Case and chose to upload via Sample Bulk Upload or Navigate to the organization assets section, from the top right menu (opens by clicking on your profile account)
Click on "Bulk Import" to open the sample import wizard
Fill in the sample details, and choose the appropriate assay type (if no assay is configured for your sample, select "None" as an option)
3. Add the S3 Bucket from the Upload Wizard
4. You could select folders to start a bulk upload of all FASTQ \ VCF files from a folder
5. Or select specific files from a list of files
6.Data Type: Select the type of sample you would like to upload
7.Add Data:
8.Add Subject: Select 'Subject Name' or add a new subject
New subject, All added information (Year of birth, diagnosis, etc..) will be tagged to the sample and serve as future referenceClick Next - The sample will start uploading.
Still have questions? Reach out to our Support Team, they'll be happy to help!