Unable to install bioconda and bowtie
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9 weeks ago
➜  ~ conda install -c "bioconda/label/cf201901" bowtie

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - bowtie

Current channels:

  - https://conda.anaconda.org/bioconda/label/cf201901/osx-arm64
  - https://conda.anaconda.org/bioconda/label/cf201901/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

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.

Based on this Github post, I simply tried replacing conda with mamba in conda install -c "bioconda/label/cf201901" bowtie and I get nothing provides requested bowtie.

I think I've tried just about everything. The Bioconda homepage says, "So easy, your grandfather could do this..." At this point, I wish he could.

I'm on a Macbook M1. Just setting it up. I had all of this set up on my old laptop. I have no idea how I did it back then.

bioconda conda • 599 views
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Where did you get the command from that includes this channel: -c "bioconda/label/cf201901"? The standard way would be conda install -c bioconda bowtie or better configure the channels permanently as directed on the BioConda website. Mamba won't help you if conda doesn't find a package, it just makes some things faster. Maybe some packages are not available for M1 macs but try the default way first.

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I found the command on the Anaconda webpage.

I tried all the methods, including the one you suggested, with identical results:

Last login: Sun Sep 25 13:46:23 on ttys001
(base) ➜  ~ conda install -c bioconda bowtie
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - bowtie

Current channels:

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

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.
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I have a MacBook M1 and it works perfectly. Just properly create a conda environment and install bowtie in the default way.

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Hello, please see above for my response.

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Try this:

conda deactivate
conda activate path/to/conda/environment
conda install -c bioconda bowtie

However, is there a reason why you want to use Bowtie over Bowtie2? Otherwise, try installing Bowtie2 and see if it works.

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Same result.

I've tried the instructions exactly as mentioned here, but to no avail.

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Which python version are you running for your conda environment?

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