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How to Use My Own Method in FireCloud Workspace?

I want to use my own method (modified Seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla#) to run TCGA sample data. I could not find a suitable method in “Method Repository”, neither could I create new method. Would you please to give me some advice to figure this problem?I have approved dbGAP authorization linked to my FireCloud account.

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Answers

  • jemimalwhjemimalwh ChinaMember

    @jneff said:
    Thank you for your interest in running Seq2HLA on FireCloud.

    It may be helpful to review our recent Tool Developer Workshop_Materials. You will find exercises that go through the basic steps of adding tools to FireCloud.

    These steps include:

    1. Put a tool in a Docker container and upload to DockerHub.
    2. Create Workflow Description Language (WDL) workflow that references the tool’s docker image in DockerHub.
    3. Use Cromwell to test the WDL and dockerized tool locally.
    4. Use the FireCloud Command Line Interface (CLI) to push the tool to the FireCloud Method Repository.
    5. Run the tool on FireCloud.

    We are happy to provide guidance as you go through these steps.

    Hi! Thank you for your reply. Here I've putted the tools in a Docker image and upload this image to DockerHub. And I've tried to write the WDL according to the instruction in Broadinstitute's website (https://software.broadinstitute.org/wdl/). And I have also read the WDL scripts in FireCloud's method repository. But I'm not sure it is okay or not. The problem is that I can don't know how to test it using Cromwell. I'm using Mac OS. I don't know how to do after reading the tutorial on website (https://github.com/broadinstitute/cromwell). Would you please to help? Is there any examples that I can follow? Thank you.

    My Docker image is jemimalwh/seq2hla:v0.1

    The Workflow file is attached.

    Thank you, again.

  • jemimalwhjemimalwh ChinaMember

    @birger said:
    Have you reviewed the slides and workshop materials from the June 15th tool developers workshop (see http://gatkforums.broadinstitute.org/firecloud/discussion/7782/firecloud-itcr-tool-developers-workshop-materials-june-15th-2016#latest)? These materials provide an overview of the tool development process and some simple (e.g., "hello world") hands-on exercises. There is also a document describing the installation of tools one would use to test your WDL workflow locally. This includes docker, the wdltool toolkit (which can be used to validate the syntax of your WDL before testing it on cromwell) and the installation of a local instance of cromwell.

    Hi, Birger. Thank you for your reply. I've read the materials and have upload my method to FireCloud method repository. And I edited the method configuration and try to run, it failed.

    The error message is "Expected single value for workflow input, but evaluated result set was empty". I don't know what the problem is. Would you please to help and tell me how to configure and run my method? Thank you.

  • jemimalwhjemimalwh ChinaMember

    @birger said:
    Have you reviewed the slides and workshop materials from the June 15th tool developers workshop (see http://gatkforums.broadinstitute.org/firecloud/discussion/7782/firecloud-itcr-tool-developers-workshop-materials-june-15th-2016#latest)? These materials provide an overview of the tool development process and some simple (e.g., "hello world") hands-on exercises. There is also a document describing the installation of tools one would use to test your WDL workflow locally. This includes docker, the wdltool toolkit (which can be used to validate the syntax of your WDL before testing it on cromwell) and the installation of a local instance of cromwell.

    My input should be the RNA-seq bam files. But I don't know how to import such data. I have TCGA controlled data access, and I have linked my eRA account.

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