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setup local picard against local htsjdk

Hi picarders,

Since I am not having success using picard on my cram files, I decided to setup the picard source code along with the htsjdk source code locally, where I put htsjdk (folder with the same name) under the picard folder.

Here is the problem. I am trying to link my local htsjdk with my local picard code, but there is no documentation regarding this.

There is an old thread on this https://gatkforums.broadinstitute.org/gatk/discussion/6826/picard-build-cant-find-htsjdk, but somehow they didn't explicitly give an answer to the very question they try to answer. They provided all other links except the one that answer the question!

It is possible that I have missed the place where the answer is. Please direct me to the right direction. Thank you very much!




  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It's no longer necessary to install htsjdk manually. The build system has been updated to retrieve htsjdk automatically at build time. If you want to build with a different version of htsjdk you need to edit the gradle build script to point at the version you want. You can find some instructions for building the code in the readme document.

  • Thanks @Geraldine_VdAuwera for the kind email reply!

    The reason I need to have my own local htsjdk is because I need to modify the htsjdk code.

    Here is the reason. When I tried to run MarkDuplicates, I got an error stating that Reference sequence is not provided even though I did. So I need to go there and hard code the path and file. I know it's not the solution, but at this moment, I just need to run MarkDuplicates.

    I submitted the question "picard tool for MarkDuplicates for cram" to the board, but no answer so far. I don't think I will get the working answer within this week. Instead of waiting, just do it myself. Thanks!



  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    The error actually states that you do not provide a valid reference:

    Exception in thread "main" java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download

    Please see my reply in your other post.

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