Read bam/cram file with IGV from aws s3
2
4
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2.8 years ago
quentin54520 ▴ 120

Hi all,

We store our alignment files on aws s3. I would like to be able to open them with IGV without needing to download them completely, but I can't find an optimal solution.

If I get a pre-signed url it works but it's not convenient.

I try to follow this but I can't do it at all. I think the problem comes from the configuration file at the end, I don't know exactly what is needed or not. Knowing that we do not have a connection by google, I would just like to use our aws identifiers. When i click on login on igv and add my longin and password i receive a "succes" answer; but then nothing happen on igv, the menu "amazon --> Load from s3 bucket is still inaccessible.

i use this json (i replace the XXXX by the corresponding value):

   {
   "apiKey": "",

   "project_id": "igv",

   "auth_provider": "Amazon",
   "aws_region": "us-east-1",
   "scope": "email",
   "redirect_uris": [
     "http://localhost:60151/oauthCallback"
   ],

   "client_id": "XXXXXX",
   "client_secret": "XXXXX",
   "authorization_endpoint": "XXXXXX",
   "token_endpoint": "XXXX",
   "aws_cognito_pool_id": "XXXX",
   "aws_cognito_fed_pool_id": "",
   "aws_cognito_role_arn": "XXXXX"
}
s3 IGV aws amazon • 4.8k views
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1
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It's been on my roadmap to upgrade our current solution to using federated access. For now, we have all the alignments stored in a public S3 bucket but restrict access to certain IP addresses and VPC endpoints. It works for both IGV (end-users need to be connected via VPN) and our internal genome browser.

To limit access on S3 buckets: https://aws.amazon.com/premiumsupport/knowledge-center/block-s3-traffic-vpc-ip/

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0
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May want to ask this on IGV support forum: https://groups.google.com/g/igv-help

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2
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2.4 years ago
quentin54520 ▴ 120

if people come across this post here is some new information:

The last version of igv (2.13.0) add a native support for s3. You just have to get your credentials (programmatic acces) acces key and secret Key, put your credentials files in the good directory (usually it's ~/.aws/credentials ) and now you can click on the Amazon tab in IGV to load your files.
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3
Entering edit mode
2.8 years ago

Author of IGV's AWS S3+Cognito support here... can you elaborate on what's failing for you (share some error messages from IGV's console when running it from cmdline)?

The success message is a good sign...Did you follow the steps in:

https://umccr.org/blog/igv-amazon-backend-setup/

Make sure you review the S3 policies (paste it over here), that's a common error: working auth yet insufficient S3 perms.

The JSON you shared looks incomplete, here's our working example for our org:

https://github.com/umccr/infrastructure/tree/master/cdk/apps/igv/config/backend/dev

Also, there's the frontend docs too over here:

https://umccr.org/blog/igv-amazon-frontend-setup/

Hope that helps!
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0
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Thank you for your reply,

Yes i follow all the steps of this link.

For the json i don't know what to put on "aws_cognito_fed_pool_id" or "auth_provider_x509_cert_url" is i don't want to used federated acces, but just from the aws cognito user.

The error of IGV after click on "amazon --> Login, add the login and password, i come back to igv and i get :

INFO [2022-01-20T17:50:03,629] [CommandListener.java:186]  GET /oauthCallback?code=30eceb29-f186-4837-b19f-791ee492c6a1&state=94093997-bbaa-4a01-b4b1-93b9dabcde18 HTTP/1.1
ERROR [2022-01-20T17:50:03,673] [OAuthProvider.java:242]  java.net.UnknownHostException: igv-laporte-team.igv-laporte-team.auth.us-east-1.amazoncognito.com
INFO [2022-01-20T17:50:04,280] [CommandListener.java:186]  GET /favicon.ico HTTP/1.1

The S3 iam role is :

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "IGVCognitoAuthedUsersProd",
            "Effect": "Allow",
            "Action": [
                "s3:ListBucket",
                "s3:GetObject"
            ],
            "Resource": [
                "arn:aws:s3:::mybucket"
            ]
        },
        {
            "Sid": "IGVListBuckets",
            "Effect": "Allow",
            "Action": [
                "s3:ListAllMyBuckets"
            ],
            "Resource": [
                "arn:aws:s3:::*"
            ]
        },
        {
            "Effect": "Allow",
            "Action": [
                "mobileanalytics:PutEvents",
                "cognito-sync:*",
                "cognito-identity:*"
            ],
            "Resource": [
                "*"
            ]
        }
    ]
}
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0
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ERROR [2022-01-20T17:50:03,673] [OAuthProvider.java:242] java.net.UnknownHostException: igv-laporte-team.igv-laporte-team.auth.us-east-1.amazoncognito.com

This hostname repetition, igv-laporte-team.igv-laporte-team. ... should be just one of those, can you double check the configs for that one?

Also make sure you download the .json.gz oauth-config file I pointed above and compare it with yours.

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0
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i managed this error but now i'm able to see my list of bucket but when i choose a cram file and click on load i get an error :

Unexpected error: null (Service: S3, Status Code: 403, Request ID: null, Extended Request ID: s27xAGqHihSGR+CZw+v5gQO9bO5r2XflepSrLWflIr4UBODw7ktoUYmxMBVWeiJ9aSGx+PZYV84=). See igv.log for more details

The complete log of igv :

INFO [2022-01-21T17:56:16,381] [MessageUtils.java:76]  <html>Unexpected error: null (Service: S3, Status Code: 403, Request ID: null, Extended Request ID: s27xAGqHihSGR+CZw+v5gQO9bO5r2XflepSrLWflIr4UBODw7ktoUYmxMBVWeiJ9aSGx+PZYV84=).<br>See igv.log for more details
ERROR [2022-01-21T17:56:16,384] [LongRunningTask.java:75]  Exception running task
software.amazon.awssdk.services.s3.model.S3Exception: null (Service: S3, Status Code: 403, Request ID: null, Extended Request ID: s27xAGqHihSGR+CZw+v5gQO9bO5r2XflepSrLWflIr4UBODw7ktoUYmxMBVWeiJ9aSGx+PZYV84=)
    at software.amazon.awssdk.protocols.xml.internal.unmarshall.AwsXmlPredicatedResponseHandler.handleErrorResponse(AwsXmlPredicatedResponseHandler.java:156) ~[aws-xml-protocol-2.15.9.jar:?]
    at software.amazon.awssdk.protocols.xml.internal.unmarshall.AwsXmlPredicatedResponseHandler.handleResponse(AwsXmlPredicatedResponseHandler.java:106) ~[aws-xml-protocol-2.15.9.jar:?]
    at software.amazon.awssdk.protocols.xml.internal.unmarshall.AwsXmlPredicatedResponseHandler.handle(AwsXmlPredicatedResponseHandler.java:84) ~[aws-xml-protocol-2.15.9.jar:?]
    at software.amazon.awssdk.protocols.xml.internal.unmarshall.AwsXmlPredicatedResponseHandler.handle(AwsXmlPredicatedResponseHandler.java:42) ~[aws-xml-protocol-2.15.9.jar:?]
    at software.amazon.awssdk.awscore.client.handler.AwsSyncClientHandler$Crc32ValidationResponseHandler.handle(AwsSyncClientHandler.java:94) ~[aws-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseClientHandler.lambda$successTransformationResponseHandler$5(BaseClientHandler.java:229) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.HandleResponseStage.execute(HandleResponseStage.java:40) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.HandleResponseStage.execute(HandleResponseStage.java:30) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptTimeoutTrackingStage.execute(ApiCallAttemptTimeoutTrackingStage.java:73) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptTimeoutTrackingStage.execute(ApiCallAttemptTimeoutTrackingStage.java:42) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.TimeoutExceptionHandlingStage.execute(TimeoutExceptionHandlingStage.java:77) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.TimeoutExceptionHandlingStage.execute(TimeoutExceptionHandlingStage.java:39) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptMetricCollectionStage.execute(ApiCallAttemptMetricCollectionStage.java:50) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallAttemptMetricCollectionStage.execute(ApiCallAttemptMetricCollectionStage.java:36) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.RetryableStage.execute(RetryableStage.java:64) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.RetryableStage.execute(RetryableStage.java:34) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.StreamManagingStage.execute(StreamManagingStage.java:56) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.StreamManagingStage.execute(StreamManagingStage.java:36) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.executeWithTimer(ApiCallTimeoutTrackingStage.java:80) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.execute(ApiCallTimeoutTrackingStage.java:60) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallTimeoutTrackingStage.execute(ApiCallTimeoutTrackingStage.java:42) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallMetricCollectionStage.execute(ApiCallMetricCollectionStage.java:48) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ApiCallMetricCollectionStage.execute(ApiCallMetricCollectionStage.java:31) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.RequestPipelineBuilder$ComposingRequestPipelineStage.execute(RequestPipelineBuilder.java:206) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ExecutionFailureExceptionReportingStage.execute(ExecutionFailureExceptionReportingStage.java:37) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.pipeline.stages.ExecutionFailureExceptionReportingStage.execute(ExecutionFailureExceptionReportingStage.java:26) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.http.AmazonSyncHttpClient$RequestExecutionBuilderImpl.execute(AmazonSyncHttpClient.java:193) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.invoke(BaseSyncClientHandler.java:133) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.doExecute(BaseSyncClientHandler.java:159) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.lambda$execute$1(BaseSyncClientHandler.java:112) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.measureApiCallSuccess(BaseSyncClientHandler.java:167) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.internal.handler.BaseSyncClientHandler.execute(BaseSyncClientHandler.java:94) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.core.client.handler.SdkSyncClientHandler.execute(SdkSyncClientHandler.java:45) ~[sdk-core-2.15.9.jar:?]
    at software.amazon.awssdk.awscore.client.handler.AwsSyncClientHandler.execute(AwsSyncClientHandler.java:55) ~[aws-core-2.15.9.jar:?]
    at software.amazon.awssdk.services.s3.DefaultS3Client.headObject(DefaultS3Client.java:4875) ~[s3-2.15.9.jar:?]
    at org.broad.igv.util.AmazonUtils.getObjectMetadata(AmazonUtils.java:211) ~[igv.jar:?]
    at org.broad.igv.util.AmazonUtils.isObjectAccessible(AmazonUtils.java:252) ~[igv.jar:?]
    at org.broad.igv.aws.S3LoadDialog.lambda$loadButtonActionPerformed$0(S3LoadDialog.java:106) ~[igv.jar:?]
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72) [igv.jar:?]
    at java.util.concurrent.FutureTask.run(Unknown Source) [?:?]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:?]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:?]
    at java.lang.Thread.run(Unknown Source) [?:?]
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0
Entering edit mode

Oh this time the issue was the IAM, now it's work ! Thanks you so much

The only point that i found strange is that after the first login, if i restart my computer i can log in without enter my password. It's normal ? I made a mistake in the configuration ?

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0
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Great to hear!

What was the problem with IAM? Can you describe how you solved that a bit more?

If you haven't closed IGV or if your computer's OS session management restores processes as they were, yes, the temporal access creds are stored within IGV's process memory.

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Thanks for you assistance Roman, as always. Just a reminder that you can always open an issue at https://github.com/igvteam/igv/issues. I personally don't have time to scan biostars regularly.

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First I had a problem of misunderstanding what is "aws_cognito_fed_pool_id" now it's fixed. The only difference with your config file is that I left "auth_provider_x509_cert_url" empty.

For the iam role i forgot the second line in the the field "ressource" of the sid "IGVCognitoAuthedUsersProd" .

Another point that has nothing to do with the error: I left the configuration file on my computer rather than putting it in a public bucket.

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "IGVCognitoAuthedUsersProd",
            "Effect": "Allow",
            "Action": [
                "s3:ListBucket",
                "s3:GetObject"
            ],
            "Resource": [
                "arn:aws:s3:::mybucket",
                "arn:aws:s3:::mybucket/*"
            ]
        },
        {
            "Sid": "IGVListBuckets",
            "Effect": "Allow",
            "Action": [
                "s3:ListAllMyBuckets"
            ],
            "Resource": [
                "arn:aws:s3:::*"
            ]
        },
        {
            "Effect": "Allow",
            "Action": [
                "mobileanalytics:PutEvents",
                "cognito-sync:*",
                "cognito-identity:*"
            ],
            "Resource": [
                "*"
            ]
        }
    ]
}
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