Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Jesse Marks
    @jaamarks
    Hi all, is this the best place to ask questions about the amazon-genomics-cli?
    Mark Schreiber
    @markjschreiber
    Yes, ask away
    Jesse Marks
    @jaamarks
    I'm getting the following error message—in the log files on CloudWatch—when I try to use a file on S3 as input.
    An error occurred (403) when calling the HeadObject operation: Forbidden
    Mark Schreiber
    @markjschreiber
    Is the object in an S3 bucket that you have declared in the data section of your context? See https://aws.github.io/amazon-genomics-cli/docs/concepts/data/ for examples.
    You should also check that the bucket isn't restricted by an access control list on the bucket itself.
    Julien Lafaye
    @jlafaye
    Hi everyone, the announcement blog post (https://aws.amazon.com/blogs/aws/new-amazon-genomics-cli-is-now-open-source-and-generally-available/) mentions WDL, Nextflow, CWL & snakemake. After looking through the github repo, it seems that only WDL & nextflow are supported. Are there any plans/community effort to add support for the last two ?
    1 reply
    Grigoriy Sterin
    @grsterin
    Hey! Is it possible to run workflows located in private repositories? For example, if I would like to run a Nextflow workflow, which is located in private Gitlab repo, is there a way to supply Gitlab credentials in some way?
    1 reply
    Jesse Marks
    @jaamarks

    On the Amazon Genomics CLI Context page there is a warning "Because the status command will only show contexts that are listed in the project YAML you should take care to destroy any running contexts before deleting them from the project YAML. "

    Suppose someone deletes the project YAML before destroying the context. Is there a way to see which contexts are deployed and have the ability to destroy them from the AWS console? I'm just thinking ahead about how I can destroy contexts that were accidentally left deployed and forgotten about. Thanks

    2 replies
    Arlind Nocaj
    @ArlindNocaj
    Hi AGC team, how can I add a custom workflow, e.g. a nextflow folder from an s3 bucket, is it enough to e.g. modify "mainWorkflowURL": "https://github.com/nextflow-io/rnaseq-nf.git"? Do I have to put in a public workflow here?
    1 reply
    Arlind Nocaj
    @ArlindNocaj
    Dear agc team, enterprises, as recommended by AWS, enforce S3 Server Side Encryption, which currently is not supported by CDK, please +1 the first entry in this issue, to make make awareness for cdk, so that more customers can use AGC: aws/aws-cdk#11265
    1 reply