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Download GATK using wget?

bbimberbbimber HomeMember

I have a scripted process we use to provision development and pipeline machines. This includes scripts to download and install various tools, typically using wget from a public download location. Is there anything like this possible w/ GATK? Are there tricks that allow me to authenticate against your download URL using wget (or similar), and/or is there a public download page anymore? Thanks in advance.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    I don't think that will be possible using the distribution download page, because you have to be logged in to the forum and accept the licensing terms explicitly.

    What you could do is have your script retrieve the source from our github repository and build the jar in place, but it's a more lengthy process.

  • bbimberbbimber HomeMember

    thanks for the reply. i was exploring this; however, it's a considerably longer process and introduces some other dependencies not otherwise needed.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I agree it's not a very appealing solution. If it was me I'd set up a local server with a copy of the jar (downloaded there manually), which any machine on the network can then retrieve.

  • AlexanderVAlexanderV BerlinMember

    But is it legal - according to the current licence - to distribute publicly a copy of the GATK (version 3.4 in this case)?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It is legal to do this within the boundaries of your institution, if the institution representative has agreed to the license. E.g. the IT department can make the software available for the researchers in various departments. You just can't make it available to users outside the institution.

  • yjx1217yjx1217 NiceMember

    Hello, I want to check whether it is OK now to put GATK (v3.8) to the public domain for easier downloading with wget given that no registration is needed anymore to download GATK from the GATK website. Thanks in advance!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @yjx1217 We want to enable that but we still have some paperwork to do to make that 100% ok legally. So for now, technically the answer is no (for 3.x versions). You're welcome to do that with any of the 4.x version however.

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