Several attempts at installation fail

[terrycojones]

I just tried to follow the installation instructions at https://usher-wiki.readthedocs.io/en/latest/QuickStart.html I tried three things, none of which worked.

1. Following the Quick install commands, conda install usher fails:

$ conda install usher
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - usher

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda
  - defaults

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

2. I then tried the conda local build / git clone approach, and three required packages are not found:

$ conda env create -f environment.yml
                                   conda activate usher
Channels:
 - conda-forge
 - bioconda
 - anaconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - isa-l
  - mafft
  - protobuf=3.12.3*

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/anaconda/osx-arm64
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/r/osx-arm64

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

3. After that I used brew install docker (I'm on OS X) to install docker, and got this when following the install instructions

$ docker pull pathogengenomics/usher:latest
Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?

in this final case I guess I need to start a daemon somehow (it would be good if your instructions mentioned this).

4. I didn't try the other "Installation scripts" approach, because Mac OS installation script seems broken #369 leads me to think that it won't work, either.

[liamxg]

Dear @terrycojones,

Me too.

conda install usher
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): failed

NotWritableError: The current user does not have write permissions to a required path.
path: /Users/liam/opt/miniconda3/pkgs/cache/3e39a7aa.json
uid: 501
gid: 20

[yatisht]

Did you run all commands listed in the instructions:

# Create a new environment for UShER
conda create -n usher-env
# Activate the newly created environment
conda activate usher-env
# Set up channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# Install the UShER package
conda install usher

I tried it just now and it works fine.

[liamxg]

I have tried, but does't works for me.

[terrycojones]

Yes, I followed the commands exactly.

[AngieHinrichs]

@terrycojones I think this part of the conda install output is the main sticking point for now:

Platform: osx-arm64

Your Mac has an M series CPU (arm64 architecture), and the usher package needs some updates in order to compile successfully on arm64.

I have not tried running in docker, but @aofarrel has reported success with that and might be able to offer suggestions?