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How do you download GATK using ansible script?

serineserine MelbourneMember

I've been fighting this for a little while and I think this is something you should consider strongly if you haven't already. How can one download GATK set of tools non interactively e.g with wget command ?

In order to install GATK set of tools, one can download .jar file, which is pretty easy, but one needs to accept some LICENCE thingo and register with loging to proceed. This is fine for casual user to mark around with point and click, but how do you propose one does that in more efficient way?

You can imaging that most users (at least in my opinion) will need some sort of server, so downloading it localy and then scping it over to the server isn't particular efficient right? Bear minimum there should be a download url after one accepted the licence, so that user can wget the .jar file.

A step further would be enabling users to wget and accept licence agrement in one step. Something along this line I guess wget --no-cookies --no-check-certificate --header "Cookie: gpw_e24=http%3A%2F%2Fwww.oracle.com%2F; oraclelicense=accept-securebackup-cookie" "http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz"

We have 4 servers that we need to keep in sync, which we use ansible script for. We download GATK .jar localy once and then use that, but this isn't particular efficient as I've mentioned before.

I've have attempted previously to compile from souce, but couldn't get it to work. I've asked that question here and even though I thought I found the error. I later tested it out with oracle java and it still didn't compile.

I look forward hearing your opinion on this issues.

Kirill

Best Answer

Answers

  • serineserine MelbourneMember

    Hi Geraldine,

    Thanks for reply. I look forward to new system.

    Cheers

  • Hai,
    Most GATK4 tools have fairly simple software requirements: a Unix-style OS and Java 1.8. However, a subset of tools have additional R and/or Python dependencies. These dependencies (as well as the base system requirements). So we strongly recommend using the Docker container system, if that's an option on your infrastructure, rather than a custom installation. All released versions of GATK4 can be found as prepackaged container images in Dockerhub. If you can't use Docker, do yourself a favor and use the Conda environment that we provide to manage dependencies. If you run into a pip error and also recently updated your Mac OS, you can use.

    Regards,
    Riya.
    developer

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