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Fail to set up conda environment for GATK with the gatkcondaenv.yml file

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5 comments

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    Tiffany Miller

    Hi fanwayne , I will see if I can recreate this. Did you follow these instructions?

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    fanwayne

    Hi Tiffany, many thanks for your support. I think I have just fixed this issue. This may be a connecting issue. I added severall alternative channels to the file .condarc and changed the mirror for pip command. The gatk envrionment was successfully created after I retried several times of the command "conda env create -n gatk -f gatkcondaenv.yml".

    The bottom of the log showed the following text and I can activate the gatk through conda now. Thank you.

    #
    # To activate this environment, use
    #
    # $ conda activate gatk
    #
    # To deactivate an active environment, use
    #
    # $ conda deactivate

     

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    NawarDalila

    Hi fanwayne,

    Would you please share the channels that you used and how exactly you did that? 

    Many thanks in advance

    Nawar

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    fanwayne

    Hi NawarDalila. I'm not sure whether the following channels would work in countries other than China.

    Below are the details in my .condarc under the home path.

    auto_activate_base: false
    ssl_verify: true
    channels:
    - conda-forge
    - bioconda
    - defaults
    - https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
    - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
    - https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
    show_channel_urls: true

    I also changed the pip mirror with the following commands.

    mkdir ~/.pip
    vim ~/.pip/pip.conf
    [global]
    index-url = https://mirrors.cloud.tencent.com/pypi/simple

    By the way, I changed "- anaconda::tensorflow=1.12.0=mkl_py36h69b6ba0_0" with
    "- anaconda::tensorflow=1.12.0=mkl_py36h2b2bbaf_0" in the gatkcondaenv.yml file.

     

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    NawarDalila

    Thank you very much for sharing. I will try and see what happens.

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