conda installation problem

Installation of 0.8.0 using bioconda:

conda create -n deepvariant deepvariant

fails on CentOS 6.6 with:

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/.travis.yml'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/README.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/documentation/Makefile'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/documentation/conf.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/documentation/index.rst'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/setup.cfg'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/setup.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/six.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/test_six.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/six/tox.ini'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/socksipy-branch/setup.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/platform/gsutil/third_party/socksipy-branch/socks.pyc'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/rpm/mapping/command_mapping.yaml'
specified in the package manifest cannot be found.

CondaVerificationError: The package for google-cloud-sdk located at /home/pedge/anaconda3/pkgs/google-cloud-sdk-243.0.0-py27_0
appears to be corrupted. The path 'share/google-cloud-sdk-243.0.0-0/rpm/mapping/component_mapping.yaml'
specified in the package manifest cannot be found.

(there are many similar CondaVerificationErrors before this) Conda info:

     active environment : longshot
    active env location : /home/pedge/anaconda3/envs/longshot
            shell level : 2
       user config file : /home/pedge/.condarc
 populated config files : /home/pedge/.condarc
          conda version : 4.6.9
    conda-build version : 3.17.6
         python version : 3.7.1.final.0
       base environment : /home/pedge/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/OpenMDAO/linux-64
                          https://conda.anaconda.org/OpenMDAO/noarch
          package cache : /home/pedge/anaconda3/pkgs
                          /home/pedge/.conda/pkgs
       envs directories : /home/pedge/anaconda3/envs
                          /home/pedge/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.9 requests/2.21.0 CPython/3.7.1 Linux/2.6.32-696.18.7.el6.x86_64 centos/6.6 glibc/2.12
                UID:GID : 511626:8162
             netrc file : None
           offline mode : False

[chapmanb]

Anna; Apologies about the issues. If you also include the conda-forge channel in your install it should resolve cleanly:

conda create -n deepvariant -c conda-forge -c bioconda python=2.7 deepvariant

bioconda is heavily dependent on conda-forge packages so you’ll want to include that whenever installing anything from bioconda to ensure all the dependencies are available. Hope this helps get it running for you.

[pristanna]

DeepVariant Installation problem using Anaconda version 4.8.2 https://anaconda.org/bioconda/deepvariant

Tried to installed with default python version which is Python 3.7.6

conda activate deepvariant
conda install -c bioconda deepvariant

Output:

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                                                                                                                                                                                                      failed                                                                                                                                                                                                                                                                          
UnsatisfiableError: 

Second option with the label

conda install -c bioconda/label/cf201901 deepvariant

Output:

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                                                                                                                                                                                                      failed                                                                                                                                                                                                                                                                          
UnsatisfiableError:

Noticed that required version is 2.7 so I removed the environment and tried to install it with this version

conda remove --name deepvariant --all conda create -n deepvariant python=2.7 deepvariant

Output:

Collecting package metadata (repodata.json): done
Solving environment: - 
Found conflicts! Looking for incompatible packages.                                                                                                                                                                                                                         failed                                                                                                                                                                                                                                                                          
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package python conflicts for:
python=2.7
deepvariant -> python[version='2.7.*|>=2.7,<2.8.0a0']
deepvariant -> boost -> python[version='3.4.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.6|3.7.*']

After reading this issue: https://github.com/google/deepvariant/issues/177, I tried to constrain google-cloud-sdk version

conda create -n deepvariant python=2.7 deepvariant 'google-cloud-sdk<243.0.0'

Output:

Collecting package metadata (repodata.json): done
Solving environment: / Found conflicts! Looking for incompatible packages.                                                                                                                                                                                                                         failed                                                                                                                                                                                                                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package google-cloud-sdk conflicts for:
google-cloud-sdk[version='<243.0.0']
deepvariant -> google-cloud-sdk

Package python conflicts for:
python=2.7
deepvariant -> python[version='2.7.*|>=2.7,<2.8.0a0']
google-cloud-sdk[version='<243.0.0'] -> python=2.7
deepvariant -> boost -> python[version='3.4.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.6|3.7.*']

Package setuptools conflicts for:
deepvariant -> protobuf -> setuptools
python=2.7 -> pip -> setuptools

I also tried to install clean environment with Python 2.7 before installing deepvariant

conda create -n deepvariant  python=2.7
conda activate deepvariant
conda install -c bioconda deepvariant

Output:

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | Found conflicts! Looking for incompatible packages.                                                                                                                                                                                                                         failed                                                                                                                                                                                                                                                                          

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - deepvariant -> python[version='3.4.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.6|3.7.*']

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

Do you have any idea what is causing the problem and how to proceed, please?