Can;t install staramr, blast not found.

[Abelcanc3rhack3r]

I tried installing via mamba:

conda install mamba mamba install -c bioconda -c conda-forge -c defaults staramr==0.7.2 pandas==1.1.5 mlst==2.19.0

Then it gives this output: Looking for: ['staramr==0.7.2', 'pandas==1.1.5', 'mlst==2.19.0']

bioconda/win-64 Using cache bioconda/noarch Using cache conda-forge/win-64 Using cache conda-forge/noarch Using cache pkgs/main/noarch No change pkgs/main/win-64 No change pkgs/r/win-64 No change pkgs/msys2/win-64 No change pkgs/r/noarch No change pkgs/msys2/noarch No change

Pinned packages:

• python 3.8.*

Encountered problems while solving:

• nothing provides blast >=2.2.31 needed by staramr-0.7.2-py_0
• nothing provides blast >=2.9.0 needed by mlst-2.19.0-0

[apetkau]

Hello @Abelcanc3rhack3r

From the win-64 messages above, I am assuming you are trying to install starmar on Windows using conda? Unfortunately, staramr depends on packages found through the bioconda project (https://bioconda.github.io/index.html), which does not explicitly support Windows (though some packages might still work on Windows).

A few options you would have to install starmar on Windows would be:

1. Install the dependencies outside of conda (https://github.com/phac-nml/staramr#dependencies). This might require a lot of effort to get everything working though.
2. You could try out the Docker container found at https://quay.io/repository/biocontainers/staramr?tab=info (this is built automatically from the conda package).
3. You could try using Windows Subsystems for Linux (https://ubuntu.com/wsl) or a virtual machine to get a Linux environment installed on Windows, and then proceed through installing via conda above.

I hope this helps.

[Abelcanc3rhack3r]

Hi Aaron, Yes I'm using Windows.

So you are saying I must Install everything on the Linux environment?

The mamba install command will take care of all the dependencies in the Linux environment including the blast?

Thank you

On Tue, Apr 5, 2022, 22:05 Aaron Petkau @.***> wrote:

Hello @Abelcanc3rhack3r https://github.com/Abelcanc3rhack3r

From the win-64 messages above, I am assuming you are trying to install starmar on Windows using conda? Unfortunately, staramr depends on packages found through the bioconda project ( https://bioconda.github.io/index.html), which does not support Windows.

A few options you would have to install starmar on Windows would be:

1. Install the dependencies outside of conda ( https://github.com/phac-nml/staramr#dependencies). This might require a lot of effort to get everything working though.
2. You could try out the Docker container found at https://quay.io/repository/biocontainers/staramr?tab=info (this is built automatically from the conda package).
3. You could try using Windows Subsystems for Linux ( https://ubuntu.com/wsl) or a virtual machine to get a Linux environment installed on Windows, and then proceed through installing via conda above.

I hope this helps.

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