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Meta: extracting available programs and parameters from GenomeAnalysisTK.jar

lindenblindenb FranceMember ✭✭

Hi GATK,

a 'meta' question:

As the programs in GATK are java classes described with java annotation, I wonder if there is an automatic way to collect all the available programs and their parameters (option, description, optional ... ) as a structured output ?

I imagine https://www.broadinstitute.org/gatk/gatkdocs/ is built using such tool isn't t ?

thanks.

Pierre

Tagged:

Issue · Github
by Sheila

Issue Number
302
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answers

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    By the way, my answer assumes you're interested in the structured output, not the details of the system itself. If you're actually interested in the system to apply it in another project, it is part of the open-source framework package and I can point you to the relevant code. It's a bit convoluted (as is everything in GATK code) but very convenient.

  • lindenblindenb FranceMember ✭✭

    That's great! Many thanks Geraldine !

  • lindenblindenb FranceMember ✭✭

    Geraldine, to answer your last comment, I'm currently working on a GUI-based tool to help my colleagues+biologists to use some GATK tools without knowledge of the command line.

    I plan to release it as a JNLP application inside my lab.

    On a license/property point of view, can I release it on a public server ?

    Is there any legal problem in writing a short paper about this tool that would wrap the GATK ?

    Issue · Github
    by Sheila

    Issue Number
    307
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • lindenblindenb FranceMember ✭✭
    edited November 2015

    If you're actually interested in the system to apply it in another project, it is part of the open-source framework package and I can point you to the relevant code. It's a bit convoluted (as is everything in GATK code) but very convenient.

    yes, please :-)

    I'd rather use the java code rather than parsing the JSON files where the schema/location might change in the future.

    I found something under https://github.com/broadgsa/gatk/tree/master/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/help but it's not clear how I should use this class from a main method to get all the available tools.

    Thanks !

  • lindenblindenb FranceMember ✭✭

    many thanks again

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