Install precompiled binaries

Hello, I’m writing you because I’m trying to install deepvariant, but I’m encountering several difficulties in doing so. I’ve tried at first to install through anaconda (conda install -c bioconda deepvariant), but I alway get the same problem:

    Traceback (most recent call last):
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 497, in run_script
        subprocess_call(command_args, env=env, path=dirname(path))
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/gateways/subprocess.py", line 56, in subprocess_call
        output=_format_output(command_str, path, rc, stdout, stderr))
    subprocess.CalledProcessError: Command '['/bin/bash', '-x', '/PATH/TO/MY/FOLDER/Andrea/myanaconda/deepvariant/bin/.deepvariant-post-link.sh']' returned non-zero exit status 1.
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 327, in _execute_actions
        run_script(target_prefix, Dist(pkg_data), 'post-unlink' if is_unlink else 'post-link')
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 513, in run_script
        raise LinkError(message)
    conda.exceptions.LinkError: post-link script failed for package bioconda::deepvariant-0.9.0-py27h7333d49_0
    running your command again with `-v` will provide additional information
    location of failed script: /PATH/TO/MY/FOLDER/Andrea/myanaconda/deepvariant/bin/.deepvariant-post-link.sh
    ==> script messages <==
    <None>
    
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 281, in execute
        pkg_data, actions)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 344, in _execute_actions
        reverse_excs,
    conda.CondaMultiError: post-link script failed for package bioconda::deepvariant-0.9.0-py27h7333d49_0
    running your command again with `-v` will provide additional information
    location of failed script: /PATH/TO/MY/FOLDER/Andrea/myanaconda/deepvariant/bin/.deepvariant-post-link.sh
    ==> script messages <==
    <None>
    
    
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/cli/main.py", line 140, in _main
        exit_code = args.func(args, p)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/cli/install.py", line 326, in install
        execute_actions(actions, index, verbose=not context.quiet)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/plan.py", line 828, in execute_actions
        execute_instructions(plan, index, verbose)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/instructions.py", line 247, in execute_instructions
        cmd(state, arg)
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/instructions.py", line 108, in UNLINKLINKTRANSACTION_CMD
        txn.execute()
      File "/exports/applications/apps/SL7/anaconda/5.0.1/lib/python3.6/site-packages/conda/core/link.py", line 297, in execute
        rollback_excs,
    conda.CondaMultiError: post-link script failed for package bioconda::deepvariant-0.9.0-py27h7333d49_0
    running your command again with `-v` will provide additional information
    location of failed script: /PATH/TO/MY/FOLDER/Andrea/myanaconda/deepvariant/bin/.deepvariant-post-link.sh
    ==> script messages <==
    <None>

Hovewer, since conda installed successfully all the dependencies, I’ve then tried to download the precompiled binaries and use them, but couldn’t find a guide on how to install them. Is there a page where to find guidelines on how to install the precompiled deepvariant? If not, is there a way to fix the anaconda environment issue?

Thank you in advance,

Andrea

[serge2016]

@PlatonB, https://github.com/google/deepvariant/issues/258#issuecomment-573807042

[pichuan]

@serge2016 @PlatonB Thank you for raising this issue again. We’re now aiming for an earlier release, in March. I’ll also update to the other issue.